[med-svn] [bcftools] 01/06: Imported Upstream version 1.3

Afif Elghraoui afif-guest at moszumanska.debian.org
Tue Feb 2 08:04:41 UTC 2016


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afif-guest pushed a commit to branch master
in repository bcftools.

commit 202ee545ae064fe526d89cc184f5eb506ff68e69
Author: Afif Elghraoui <afif at ghraoui.name>
Date:   Mon Feb 1 19:50:51 2016 -0800

    Imported Upstream version 1.3
---
 AUTHORS                                    |    2 +
 HMM.c                                      |   81 +-
 HMM.h                                      |   57 +-
 Makefile                                   |   66 +-
 bcftools.h                                 |    8 +
 call.h                                     |   22 +-
 ccall.c                                    |    7 +-
 consensus.c                                |   11 +-
 convert.c                                  |  106 +-
 convert.h                                  |    6 +
 doc/bcftools.1                             |  719 ++++-
 doc/bcftools.html                          |  493 +++-
 doc/bcftools.txt                           |  463 +++-
 filter.c                                   |  187 +-
 filter.h                                   |    1 +
 gvcf.c                                     |  190 +-
 gvcf.h                                     |   41 +
 main.c                                     |    6 +-
 mcall.c                                    |  198 +-
 peakfit.c                                  |  599 ++++
 peakfit.h                                  |   49 +
 ploidy.c                                   |   41 +-
 ploidy.h                                   |   14 +-
 plot-vcfstats                              |   58 +-
 plugins/color-chrs.c                       |  559 ++++
 plugins/color-chrs.mk                      |    2 +
 plugins/color-chrs.pl                      |  528 ++++
 plugins/dosage.c                           |    2 +-
 plugins/fill-tags.c                        |  262 ++
 plugins/fixploidy.c                        |    7 +-
 plugins/fixploidy.mk                       |    4 +-
 plugins/impute-info.c                      |  163 ++
 plugins/mendelian.c                        |  248 ++
 plugins/setGT.c                            |  223 ++
 plugins/tag2tag.c                          |   36 +-
 plugins/vcf2sex.c                          |  305 +-
 plugins/vcf2sex.mk                         |    4 +-
 polysomy.c                                 |  646 +++--
 rbuf.h                                     |   25 +-
 test/annotate4.out                         |    2 +-
 test/annotate5.out                         |    4 +-
 test/{merge.2.b.vcf => annotate9.out}      |   15 +-
 test/{merge.2.b.vcf => annotate9.vcf}      |   14 +-
 test/annots9.tab                           |    5 +
 test/{merge.2.b.vcf => annots9.vcf}        |   14 +-
 test/check.chk                             |   11 +-
 test/check.vcf                             |    7 +-
 test/{check.chk => check_merge.chk}        |   57 +-
 test/consensus.5.out                       |   20 +
 test/consensus2.1.out                      |   10 +
 test/consensus2.2.out                      |   12 +
 test/consensus2.fa                         |   10 +
 test/consensus2.vcf                        |    9 +
 test/convert.gs.gt.gen                     |    2 +-
 test/convert.gt.noHead.vcf                 |   36 +
 test/convert.gt.vcf                        |   43 +
 test/convert.gvcf.out                      |  726 +++--
 test/convert.gvcf.vcf                      |  116 +-
 test/convert.hls.gt.hap                    |   35 +
 test/convert.hls.gt.legend                 |   36 +
 test/convert.hls.gt.samples                |   11 +
 test/convert.hs.gt.hap                     |   35 +
 test/convert.hs.gt.samples                 |   12 +
 test/fill-tags.out                         |   40 +
 test/filter.10.out                         |   11 +
 test/{merge.2.b.vcf => filter.11.out}      |   12 +-
 test/filter.4.vcf                          |   10 +
 test/filter.9.out                          |    1 +
 test/gvcf.fa                               |    9 +
 test/gvcf.fa.fai                           |    1 +
 test/many.alleles.trim.out                 |   10 +
 test/many.alleles.vcf                      |    7 +
 test/merge.2.b.vcf                         |    2 +-
 test/{annotate5.out => missing.vcf}        |   11 +-
 test/mpileup.2.out                         |   27 +-
 test/{mpileup.cAls.out => mpileup.X.out}   |   17 +-
 test/mpileup.X.vcf                         | 4127 ++++++++++++++++++++++++++++
 test/mpileup.c.1.out                       |   43 +
 test/mpileup.c.X.out                       |   43 +
 test/mpileup.c.X.vcf                       | 4127 ++++++++++++++++++++++++++++
 test/{mpileup.vcf => mpileup.c.vcf}        |    0
 test/mpileup.cAls.out                      |    7 +
 test/mpileup.ped                           |    3 +
 test/mpileup.ploidy                        |    4 +
 test/mpileup.samples                       |    3 +
 test/mpileup.tab                           |    7 +
 test/mpileup.vcf                           |   14 +-
 test/norm.fa                               |    2 +
 test/norm.fa.fai                           |    1 +
 test/norm.merge.2.out                      |   38 +
 test/norm.merge.2.vcf                      |   41 +
 test/norm.merge.3.out                      |   34 +
 test/norm.merge.3.vcf                      |   37 +
 test/norm.merge.out                        |    2 +-
 test/norm.merge.strict.out                 |    2 +-
 test/norm.merge.vcf                        |    2 +-
 test/norm.out                              |    2 +-
 test/norm.setref.out                       |   45 +
 test/norm.setref.vcf                       |   45 +
 test/norm.split.2.out                      |  107 +
 test/norm.split.2.vcf                      |   85 +
 test/{norm.out => norm.split.and.norm.out} |   33 +-
 test/norm.split.out                        |   11 +-
 test/norm.split.vcf                        |    6 +-
 test/norm.vcf                              |    2 +-
 test/query.18.out                          |    2 +
 test/query.19.out                          |    3 +
 test/query.20.out                          |    2 +
 test/query.21.out                          |    3 +
 test/query.22.out                          |    2 +
 test/query.23.out                          |    3 +
 test/stats.chk                             |   24 +-
 test/test-rbuf.c                           |    2 +-
 test/test.pl                               |   85 +-
 test/view.9.out                            |    4 -
 test/view.GL.vcf                           |   29 +
 test/view.PL.vcf                           |   29 +
 test/view.dropgenotypes.noheader.out       |    5 +
 test/view.dropgenotypes.out                |   12 +
 test/view.filter.annovar.1.out             |    2 +
 test/view.filter.annovar.2.out             |    1 +
 test/view.filter.annovar.3.out             |    1 +
 test/view.filter.annovar.vcf               |   52 +
 vcfannotate.c                              |  138 +-
 vcfcall.c                                  |  584 ++--
 vcfcnv.c                                   |  826 ++++--
 vcfconcat.c                                |  132 +-
 vcfconvert.c                               |  159 +-
 vcffilter.c                                |   37 +-
 vcfgtcheck.c                               |   32 +-
 vcfindex.c                                 |    8 +-
 vcfisec.c                                  |   73 +-
 vcfmerge.c                                 |   46 +-
 vcfnorm.c                                  |  931 +++----
 vcfplugin.c                                |  124 +-
 vcfquery.c                                 |   15 +-
 vcfroh.c                                   |  101 +-
 vcfstats.c                                 |  180 +-
 vcfview.c                                  |   89 +-
 vcmp.c                                     |   14 +-
 version.c                                  |    8 +
 141 files changed, 17790 insertions(+), 2680 deletions(-)

diff --git a/AUTHORS b/AUTHORS
index 412efef..3d902d4 100644
--- a/AUTHORS
+++ b/AUTHORS
@@ -4,7 +4,9 @@ Petr Danecek, Shane McCarthy and John Marshall.
 Alphabetical list of people who have made contributions:
 
     Nicholas Clarke
+    Travis Collier
     Petr Danecek <petr.danecek at sanger.ac.uk>
+    Javier Herrero
     Warren Kretzschmar <winni at well.ox.ac.uk>
     Heng Li
     Shane McCarthy <sm15 at sanger.ac.uk>
diff --git a/HMM.c b/HMM.c
index 2d2a402..9196544 100644
--- a/HMM.c
+++ b/HMM.c
@@ -1,6 +1,6 @@
 /* The MIT License
 
-   Copyright (c) 2014 Genome Research Ltd.
+   Copyright (c) 2014-2015 Genome Research Ltd.
 
    Author: Petr Danecek <pd3 at sanger.ac.uk>
 
@@ -31,6 +31,33 @@
 #include <htslib/hts.h>
 #include "HMM.h"
 
+struct _hmm_t
+{
+    int nstates;    // number of states
+
+    double *vprob, *vprob_tmp;  // viterbi probs [nstates]
+    uint8_t *vpath;             // viterbi path [nstates*nvpath]
+    double *bwd, *bwd_tmp;      // bwd probs [nstates]
+    double *fwd;                // fwd probs [nstates*(nfwd+1)]
+    int nvpath, nfwd;
+
+    int ntprob_arr;             // number of pre-calculated tprob matrices
+    double *curr_tprob, *tmp;   // Temporary arrays; curr_tprob is short lived, valid only for
+                                //  one site (that is, one step of Viterbi algorithm)
+    double *tprob_arr;          // Array of transition matrices, precalculated to ntprob_arr
+                                //  positions. The first matrix is the initial tprob matrix
+                                //  set by hmm_init() or hmm_set_tprob()
+    set_tprob_f set_tprob;      // Optional user function to set / modify transition probabilities
+                                //  at each site (one step of Viterbi algorithm)
+    void *set_tprob_data;
+    double *init_probs;         // Initial state probabilities, NULL for uniform probs
+};
+
+uint8_t *hmm_get_viterbi_path(hmm_t *hmm) { return hmm->vpath; }
+double *hmm_get_tprob(hmm_t *hmm) { return hmm->tprob_arr; }
+int hmm_get_nstates(hmm_t *hmm) { return hmm->nstates; }
+double *hmm_get_fwd_bwd_prob(hmm_t *hmm) { return hmm->fwd; }
+
 static inline void multiply_matrix(int n, double *a, double *b, double *dst, double *tmp)
 {
     double *out = dst;
@@ -63,6 +90,18 @@ hmm_t *hmm_init(int nstates, double *tprob, int ntprob)
     return hmm;
 }
 
+void hmm_init_states(hmm_t *hmm, double *probs)
+{
+    if ( !probs )
+    {
+        free(hmm->init_probs);
+        hmm->init_probs = NULL;
+    }
+
+    if ( !hmm->init_probs ) hmm->init_probs = (double*) malloc(sizeof(double)*hmm->nstates);
+    memcpy(hmm->init_probs,probs,sizeof(double)*hmm->nstates);
+}
+
 void hmm_set_tprob(hmm_t *hmm, double *tprob, int ntprob)
 {
     hmm->ntprob_arr = ntprob;
@@ -118,7 +157,10 @@ void hmm_run_viterbi(hmm_t *hmm, int n, double *eprobs, uint32_t *sites)
 
     // Init all states with equal likelihood
     int i,j, nstates = hmm->nstates;
-    for (i=0; i<nstates; i++) hmm->vprob[i] = 1./nstates;
+    if ( hmm->init_probs )
+        for (i=0; i<nstates; i++) hmm->vprob[i] = hmm->init_probs[i];
+    else
+        for (i=0; i<nstates; i++) hmm->vprob[i] = 1./nstates;
 
     // Run Viterbi
     uint32_t prev_pos = sites[0];
@@ -130,7 +172,7 @@ void hmm_run_viterbi(hmm_t *hmm, int n, double *eprobs, uint32_t *sites)
         int pos_diff = sites[i] == prev_pos ? 0 : sites[i] - prev_pos - 1;
 
         _set_tprob(hmm, pos_diff);
-        if ( hmm->set_tprob ) hmm->set_tprob(hmm, prev_pos, sites[i], hmm->set_tprob_data);
+        if ( hmm->set_tprob ) hmm->set_tprob(hmm, prev_pos, sites[i], hmm->set_tprob_data, hmm->curr_tprob);
         prev_pos = sites[i];
 
         double vnorm = 0;
@@ -182,8 +224,16 @@ void hmm_run_fwd_bwd(hmm_t *hmm, int n, double *eprobs, uint32_t *sites)
 
     // Init all states with equal likelihood
     int i,j,k, nstates = hmm->nstates;
-    for (i=0; i<nstates; i++) hmm->fwd[i] = 1./hmm->nstates;
-    for (i=0; i<nstates; i++) hmm->bwd[i] = 1./hmm->nstates;
+    if ( hmm->init_probs )
+    {
+        for (i=0; i<nstates; i++) hmm->fwd[i] = hmm->init_probs[i];
+        for (i=0; i<nstates; i++) hmm->bwd[i] = hmm->init_probs[i];
+    }
+    else
+    {
+        for (i=0; i<nstates; i++) hmm->fwd[i] = 1./hmm->nstates;
+        for (i=0; i<nstates; i++) hmm->bwd[i] = 1./hmm->nstates;
+    }
 
     // Run fwd 
     uint32_t prev_pos = sites[0];
@@ -196,7 +246,7 @@ void hmm_run_fwd_bwd(hmm_t *hmm, int n, double *eprobs, uint32_t *sites)
         int pos_diff = sites[i] == prev_pos ? 0 : sites[i] - prev_pos - 1;
 
         _set_tprob(hmm, pos_diff);
-        if ( hmm->set_tprob ) hmm->set_tprob(hmm, prev_pos, sites[i], hmm->set_tprob_data);
+        if ( hmm->set_tprob ) hmm->set_tprob(hmm, prev_pos, sites[i], hmm->set_tprob_data, hmm->curr_tprob);
         prev_pos = sites[i];
 
         double norm = 0;
@@ -222,7 +272,7 @@ void hmm_run_fwd_bwd(hmm_t *hmm, int n, double *eprobs, uint32_t *sites)
         int pos_diff = sites[n-i-1] == prev_pos ? 0 : prev_pos - sites[n-i-1] - 1;
 
         _set_tprob(hmm, pos_diff);
-        if ( hmm->set_tprob ) hmm->set_tprob(hmm, sites[n-i-1], prev_pos, hmm->set_tprob_data);
+        if ( hmm->set_tprob ) hmm->set_tprob(hmm, sites[n-i-1], prev_pos, hmm->set_tprob_data, hmm->curr_tprob);
         prev_pos = sites[n-i-1];
 
         double bwd_norm = 0;
@@ -262,8 +312,16 @@ void hmm_run_baum_welch(hmm_t *hmm, int n, double *eprobs, uint32_t *sites)
 
     // Init all states with equal likelihood
     int i,j,k, nstates = hmm->nstates;
-    for (i=0; i<nstates; i++) hmm->fwd[i] = 1./hmm->nstates;
-    for (i=0; i<nstates; i++) hmm->bwd[i] = 1./hmm->nstates;
+    if ( hmm->init_probs )
+    {
+        for (i=0; i<nstates; i++) hmm->fwd[i] = hmm->init_probs[i];
+        for (i=0; i<nstates; i++) hmm->bwd[i] = hmm->init_probs[i];
+    }
+    else
+    {
+        for (i=0; i<nstates; i++) hmm->fwd[i] = 1./hmm->nstates;
+        for (i=0; i<nstates; i++) hmm->bwd[i] = 1./hmm->nstates;
+    }
 
     // New transition matrix: temporary values
     double *tmp_xi = (double*) calloc(nstates*nstates,sizeof(double));
@@ -281,7 +339,7 @@ void hmm_run_baum_welch(hmm_t *hmm, int n, double *eprobs, uint32_t *sites)
         int pos_diff = sites[i] == prev_pos ? 0 : sites[i] - prev_pos - 1;
 
         _set_tprob(hmm, pos_diff);
-        if ( hmm->set_tprob ) hmm->set_tprob(hmm, prev_pos, sites[i], hmm->set_tprob_data);
+        if ( hmm->set_tprob ) hmm->set_tprob(hmm, prev_pos, sites[i], hmm->set_tprob_data, hmm->curr_tprob);
         prev_pos = sites[i];
 
         double norm = 0;
@@ -307,7 +365,7 @@ void hmm_run_baum_welch(hmm_t *hmm, int n, double *eprobs, uint32_t *sites)
         int pos_diff = sites[n-i-1] == prev_pos ? 0 : prev_pos - sites[n-i-1] - 1;
 
         _set_tprob(hmm, pos_diff);
-        if ( hmm->set_tprob ) hmm->set_tprob(hmm, sites[n-i-1], prev_pos, hmm->set_tprob_data);
+        if ( hmm->set_tprob ) hmm->set_tprob(hmm, sites[n-i-1], prev_pos, hmm->set_tprob_data, hmm->curr_tprob);
         prev_pos = sites[n-i-1];
 
         double bwd_norm = 0;
@@ -362,6 +420,7 @@ void hmm_run_baum_welch(hmm_t *hmm, int n, double *eprobs, uint32_t *sites)
 
 void hmm_destroy(hmm_t *hmm)
 {
+    free(hmm->init_probs);
     free(hmm->vprob);
     free(hmm->vprob_tmp);
     free(hmm->vpath);
diff --git a/HMM.h b/HMM.h
index 2fb1412..7f01245 100644
--- a/HMM.h
+++ b/HMM.h
@@ -1,6 +1,6 @@
 /* The MIT License
 
-   Copyright (c) 2014 Genome Research Ltd.
+   Copyright (c) 2014-2015 Genome Research Ltd.
 
    Author: Petr Danecek <pd3 at sanger.ac.uk>
 
@@ -31,28 +31,7 @@
 
 typedef struct _hmm_t hmm_t;
 
-typedef void (*set_tprob_f) (hmm_t *hmm, uint32_t prev_pos, uint32_t pos, void *data);
-
-struct _hmm_t
-{
-    int nstates;    // number of states
-
-    double *vprob, *vprob_tmp;  // viterbi probs [nstates]
-    uint8_t *vpath;             // viterbi path [nstates*nvpath]
-    double *bwd, *bwd_tmp;      // bwd probs [nstates]
-    double *fwd;                // fwd probs [nstates*(nfwd+1)]
-    int nvpath, nfwd;
-
-    int ntprob_arr;             // number of pre-calculated tprob matrices
-    double *curr_tprob, *tmp;   // Temporary arrays; curr_tprob is short lived, valid only for
-                                //  one site (that is, one step of Viterbi algorithm)
-    double *tprob_arr;          // Array of transition matrices, precalculated to ntprob_arr
-                                //  positions. The first matrix is the initial tprob matrix
-                                //  set by hmm_init() or hmm_set_tprob()
-    set_tprob_f set_tprob;      // Optional user function to set / modify transition probabilities
-                                //  at each site (one step of Viterbi algorithm)
-    void *set_tprob_data;
-};
+typedef void (*set_tprob_f) (hmm_t *hmm, uint32_t prev_pos, uint32_t pos, void *data, double *tprob);
 
 /**
  *   hmm_init() - initialize HMM
@@ -66,6 +45,22 @@ hmm_t *hmm_init(int nstates, double *tprob, int ntprob);
 void hmm_set_tprob(hmm_t *hmm, double *tprob, int ntprob);
 
 /**
+ *   hmm_init_states() - initial state probabilities
+ *   @probs:  initial state probabilities or NULL to reset to default
+ *
+ *   If uncalled, all states are initialized with the same likelihood
+ */
+void hmm_init_states(hmm_t *hmm, double *probs);
+
+/**
+ *   hmm_get_tprob() - return the array of transition matrices, precalculated
+ *      to ntprob positions. The first matrix is the initial tprob matrix
+ *      set by hmm_init() or hmm_set_tprob()
+ */
+double *hmm_get_tprob(hmm_t *hmm);
+int hmm_get_nstates(hmm_t *hmm);
+
+/**
  *   hmm_set_tprob_func() - custom setter of transition probabilities
  */
 void hmm_set_tprob_func(hmm_t *hmm, set_tprob_f set_tprob, void *data);
@@ -83,17 +78,26 @@ void hmm_set_tprob_func(hmm_t *hmm, set_tprob_f set_tprob, void *data);
 void hmm_run_viterbi(hmm_t *hmm, int nsites, double *eprob, uint32_t *sites);
 
 /**
+ *   hmm_get_viterbi_path() - the viterbi path: state at ith site is the
+ *      (nstates*isite)-th element
+ */
+uint8_t *hmm_get_viterbi_path(hmm_t *hmm);
+
+/**
  *   hmm_run_fwd_bwd() - run the forward-backward algorithm
  *   @nsites:   number of sites 
  *   @eprob:    emission probabilities for each site and state (nsites x nstates)
  *   @sites:    list of positions
- *
- *   When done, hmm->fwd[] contains the calculated fwd*bwd probabilities. The
- *   probability of i-th state at j-th site can be accessed as fwd[j*nstates+i].
  */
 void hmm_run_fwd_bwd(hmm_t *hmm, int nsites, double *eprob, uint32_t *sites);
 
 /**
+ *   hmm_get_fwd_bwd_prob() - the probability of i-th state at j-th site can
+ *      be accessed as fwd_bwd[j*nstates+i].
+ */
+double *hmm_get_fwd_bwd_prob(hmm_t *hmm);
+
+/**
  *   hmm_run_baum_welch() - run one iteration of Baum-Welch algorithm
  *   @nsites:   number of sites 
  *   @eprob:    emission probabilities for each site and state (nsites x nstates)
@@ -104,6 +108,7 @@ void hmm_run_fwd_bwd(hmm_t *hmm, int nsites, double *eprob, uint32_t *sites);
  *   are not updated.
  */
 void hmm_run_baum_welch(hmm_t *hmm, int nsites, double *eprob, uint32_t *sites);
+
 void hmm_destroy(hmm_t *hmm);
 
 #endif
diff --git a/Makefile b/Makefile
index 6d525eb..4357d7c 100644
--- a/Makefile
+++ b/Makefile
@@ -1,6 +1,6 @@
 # Makefile for bcftools, utilities for Variant Call Format VCF/BCF files.
 #
-#   Copyright (C) 2012-2014 Genome Research Ltd.
+#   Copyright (C) 2012-2015 Genome Research Ltd.
 #
 #   Author: Petr Danecek <pd3 at sanger.ac.uk>
 #
@@ -36,42 +36,53 @@ BGZIP  = $(HTSDIR)/bgzip
 TABIX  = $(HTSDIR)/tabix
 
 CC       = gcc
+CPPFLAGS =
 CFLAGS   = -g -Wall -Wc++-compat -O2
-DFLAGS   =
+LDFLAGS  =
+LIBS     =
+
 OBJS     = main.o vcfindex.o tabix.o \
            vcfstats.o vcfisec.o vcfmerge.o vcfquery.o vcffilter.o filter.o vcfsom.o \
            vcfnorm.o vcfgtcheck.o vcfview.o vcfannotate.o vcfroh.o vcfconcat.o \
            vcfcall.o mcall.o vcmp.o gvcf.o reheader.o convert.o vcfconvert.o tsv2vcf.o \
            vcfcnv.o HMM.o vcfplugin.o consensus.o ploidy.o version.o \
            ccall.o em.o prob1.o kmin.o # the original samtools calling
-INCLUDES = -I. -I$(HTSDIR)
+
+EXTRA_CPPFLAGS = -I. -I$(HTSDIR) -DPLUGINPATH=\"$(pluginpath)\"
+GSL_LIBS       =
 
 # The polysomy command is not compiled by default because it brings dependency
 # on libgsl. The command can be compiled wth `make USE_GPL=1`. See the INSTALL
 # and LICENSE documents to understand license implications.
 ifdef USE_GPL
-    CFLAGS += -DUSE_GPL
-    OBJS   += polysomy.o
-    LDLIBS  = -lgsl -lcblas
+    EXTRA_CPPFLAGS += -DUSE_GPL
+    OBJS += polysomy.o peakfit.o
+    GSL_LIBS = -lgsl -lcblas
 endif
 
 prefix      = /usr/local
 exec_prefix = $(prefix)
 bindir      = $(exec_prefix)/bin
+libdir      = $(exec_prefix)/lib
+libexecdir  = $(exec_prefix)/libexec
 mandir      = $(prefix)/share/man
 man1dir     = $(mandir)/man1
 
+plugindir   = $(libexecdir)/bcftools
+pluginpath  = $(plugindir)
+
 MKDIR_P = mkdir -p
 INSTALL = install -p
 INSTALL_PROGRAM = $(INSTALL)
 INSTALL_DATA    = $(INSTALL) -m 644
 INSTALL_DIR     = $(MKDIR_P) -m 755
 
+MISC_PROGRAMS = plot-vcfstats vcfutils.pl plugins/color-chrs.pl
 
 all:$(PROG) plugins
 
 # See htslib/Makefile
-PACKAGE_VERSION = 1.2
+PACKAGE_VERSION = 1.3
 ifneq "$(wildcard .git)" ""
 PACKAGE_VERSION := $(shell git describe --always --dirty)
 DOC_VERSION :=  $(shell git describe --always)+
@@ -88,7 +99,7 @@ version.h:
 force:
 
 .c.o:
-	$(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
+	$(CC) $(CFLAGS) $(EXTRA_CPPFLAGS) $(CPPFLAGS) -c -o $@ $<
 
 test: $(PROG) plugins test/test-rbuf $(BGZIP) $(TABIX)
 	./test/test.pl --exec bgzip=$(BGZIP) --exec tabix=$(TABIX)
@@ -102,8 +113,16 @@ PLUGINC = $(foreach dir, plugins, $(wildcard $(dir)/*.c))
 PLUGINS = $(PLUGINC:.c=.so)
 PLUGINM = $(PLUGINC:.c=.mk)
 
-%.so: %.c version.h version.c $(HTSDIR)/libhts.so
-	$(CC) $(CFLAGS) $(INCLUDES) -fPIC -shared -o $@ version.c $< -L$(HTSDIR) -lhts
+ifeq "$(shell uname -s)" "Darwin"
+$(PLUGINS): | bcftools
+
+PLUGIN_FLAGS = -bundle -bundle_loader bcftools
+else
+PLUGIN_FLAGS = -fPIC -shared
+endif
+
+%.so: %.c version.h version.c
+	$(CC) $(PLUGIN_FLAGS) $(CFLAGS) $(EXTRA_CPPFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $@ version.c $< $(LIBS)
 
 -include $(PLUGINM)
 
@@ -115,6 +134,7 @@ call_h = call.h $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) vcmp.h
 convert_h = convert.h $(htslib_vcf_h)
 tsv2vcf_h = tsv2vcf.h $(htslib_vcf_h)
 filter_h = filter.h $(htslib_vcf_h)
+ploidy_h = ploidy.h $(htslib_regidx_h)
 prob1_h = prob1.h $(htslib_vcf_h) $(call_h)
 roh_h = HMM.h $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(HTSDIR)/htslib/kstring.h $(HTSDIR)/htslib/kseq.h $(bcftools_h)
 cnv_h = HMM.h $(htslib_vcf_h) $(htslib_synced_bcf_reader_h)
@@ -122,7 +142,7 @@ cnv_h = HMM.h $(htslib_vcf_h) $(htslib_synced_bcf_reader_h)
 main.o: main.c $(htslib_hts_h) version.h $(bcftools_h)
 vcfannotate.o: vcfannotate.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(HTSDIR)/htslib/kseq.h $(bcftools_h) vcmp.h $(filter_h)
 vcfplugin.o: vcfplugin.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(HTSDIR)/htslib/kseq.h $(bcftools_h) vcmp.h $(filter_h)
-vcfcall.o: vcfcall.c $(htslib_vcf_h) $(HTSDIR)/htslib/kfunc.h $(htslib_synced_bcf_reader_h) $(bcftools_h) $(call_h) $(prob1_h)
+vcfcall.o: vcfcall.c $(htslib_vcf_h) $(HTSDIR)/htslib/kfunc.h $(htslib_synced_bcf_reader_h) $(HTSDIR)/htslib/khash_str2int.h $(bcftools_h) $(call_h) $(prob1_h) $(ploidy_h)
 vcfconcat.o: vcfconcat.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(HTSDIR)/htslib/kseq.h $(bcftools_h)
 vcfconvert.o: vcfconvert.c $(htslib_vcf_h) $(htslib_bgzf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) $(filter_h) $(convert_h) $(tsv2vcf_h)
 vcffilter.o: vcffilter.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) $(filter_h) rbuf.h
@@ -149,17 +169,19 @@ kmin.o: kmin.c kmin.h
 mcall.o: mcall.c $(HTSDIR)/htslib/kfunc.h $(call_h)
 prob1.o: prob1.c $(prob1_h)
 vcmp.o: vcmp.c $(htslib_hts_h) vcmp.h
-polysomy.o: polysomy.c $(htslib_hts_h)
+ploidy.o: ploidy.c $(htslib_regidx_h) $(HTSDIR)/htslib/khash_str2int.h $(HTSDIR)/htslib/kseq.h $(htslib_hts_h) $(bcftools_h) $(ploidy_h)
+polysomy.o: polysomy.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(bcftools_h) peakfit.h
+peakfit.o: peakfit.c peakfit.h $(htslib_hts_h) $(HTSDIR)/htslib/kstring.h
 consensus.o: consensus.c $(htslib_hts_h) $(HTSDIR)/htslib/kseq.h rbuf.h $(bcftools_h) $(HTSDIR)/htslib/regidx.h
 version.o: version.h version.c
 
 test/test-rbuf.o: test/test-rbuf.c rbuf.h
 
 test/test-rbuf: test/test-rbuf.o
-	$(CC) $(CFLAGS) -o $@ -lm -ldl $<
+	$(CC) $(LDFLAGS) -o $@ $^ -lm $(LIBS)
 
 bcftools: $(HTSLIB) $(OBJS)
-	$(CC) $(CFLAGS) -o $@ $(OBJS) $(HTSLIB) -lpthread -lz -lm -ldl $(LDLIBS)
+	$(CC) -rdynamic $(LDFLAGS) -o $@ $(OBJS) $(HTSLIB) -lpthread -lz -lm -ldl $(GSL_LIBS) $(LIBS)
 
 doc/bcftools.1: doc/bcftools.txt
 	cd doc && a2x -adate="$(DOC_DATE)" -aversion=$(DOC_VERSION) --doctype manpage --format manpage bcftools.txt
@@ -167,19 +189,27 @@ doc/bcftools.1: doc/bcftools.txt
 doc/bcftools.html: doc/bcftools.txt
 	cd doc && a2x -adate="$(DOC_DATE)" -aversion=$(DOC_VERSION) --doctype manpage --format xhtml bcftools.txt
 
+# make docs target depends the a2x asciidoc program
 docs: doc/bcftools.1 doc/bcftools.html
 
-install: $(PROG) doc/bcftools.1
-	$(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(man1dir)
-	$(INSTALL_PROGRAM) $(PROG) plot-vcfstats vcfutils.pl $(DESTDIR)$(bindir)
+# To avoid an install dependency on asciidoc, the make install target
+# does not depend on doc/bcftools.1
+# bcftools.1 is a generated file from the asciidoc bcftools.txt file.
+# Since there is no make dependency, bcftools.1 can be out-of-date and
+# make docs can be run to update if asciidoc is available
+install: $(PROG)
+	$(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(man1dir) $(DESTDIR)$(plugindir)
+	$(INSTALL_PROGRAM) $(PROG) $(MISC_PROGRAMS) $(DESTDIR)$(bindir)
 	$(INSTALL_DATA) doc/bcftools.1 $(DESTDIR)$(man1dir)
+	$(INSTALL_PROGRAM) plugins/*.so $(DESTDIR)$(plugindir)
 
 clean: testclean clean-plugins
 	-rm -f gmon.out *.o *~ $(PROG) version.h plugins/*.so plugins/*.P
 	-rm -rf *.dSYM plugins/*.dSYM test/*.dSYM
 
 clean-plugins:
-	-rm -f plugins/*.so plugins/*.P plugins/*.dSYM
+	-rm -f plugins/*.so plugins/*.P
+	-rm -rf plugins/*.dSYM
 
 testclean:
 	-rm -f test/*.o test/*~ $(TEST_PROG)
diff --git a/bcftools.h b/bcftools.h
index 7d3936a..6f22272 100644
--- a/bcftools.h
+++ b/bcftools.h
@@ -27,6 +27,7 @@ THE SOFTWARE.  */
 
 #include <stdarg.h>
 #include <htslib/vcf.h>
+#include <math.h>
 
 #define FT_GZ 1
 #define FT_VCF 2
@@ -60,4 +61,11 @@ static inline char gt2iupac(char a, char b)
     return iupac[(int)a][(int)b];
 }
 
+static inline double phred_score(double prob)
+{
+    if ( prob==0 ) return 99;
+    prob = -4.3429*log(prob);
+    return prob>99 ? 99 : prob;
+}
+
 #endif
diff --git a/call.h b/call.h
index 72f6fd8..bbf0a52 100644
--- a/call.h
+++ b/call.h
@@ -33,8 +33,8 @@ THE SOFTWARE.  */
 #define CALL_VARONLY        (1<<1)
 #define CALL_CONSTR_TRIO    (1<<2)
 #define CALL_CONSTR_ALLELES (1<<3)
-#define CALL_CHR_X          (1<<4)
-#define CALL_CHR_Y          (1<<5)
+//
+//
 #define CALL_FMT_GQ         (1<<6)
 #define CALL_FMT_GP         (1<<7)
 
@@ -49,15 +49,6 @@ typedef struct
 }
 family_t;
 
-typedef struct
-{
-    int min_dp, mdp;    // minimum per-sample depth of a gVCF block
-    int32_t rid, start, end, *gt, *dp;
-    char ref[2];        // reference base at start position
-    bcf1_t *line;
-}
-gvcf_t;
-
 typedef struct _ccall_t ccall_t;
 typedef struct
 {
@@ -96,12 +87,12 @@ typedef struct
     bcf1_t *rec;
     bcf_hdr_t *hdr;
     uint32_t flag;          // One or more of the CALL_* flags defined above
-    uint8_t *ploidy, all_diploid;
+    uint8_t *ploidy, all_diploid, unseen;
 
     double pl2p[256];       // PL to 10^(-PL/10) table
     int32_t *PLs;           // VCF PL likelihoods (rw)
-    int nPLs, mPLs;
-    int32_t *gts, ac[4];    // GTs and AC (w)
+    int nPLs, mPLs, nac;
+    int32_t *gts, *ac;      // GTs and AC (w)
     double *pdg;            // PLs converted to P(D|G)
     float *anno16; int n16; // see anno[16] in bam2bcf.h
     double theta;           // prior
@@ -129,9 +120,6 @@ void qcall_destroy(call_t *call);
 void call_init_pl2p(call_t *call);
 uint32_t *call_trio_prep(int is_x, int is_son);
 
-/** gVCF */
-void gvcf_write(htsFile *fh, gvcf_t *gvcf, bcf_hdr_t *hdr, bcf1_t *rec, int is_ref);
-
 void init_allele_trimming_maps(call_t *call, int als, int nals);
 void mcall_trim_numberR(call_t *call, bcf1_t *rec, int nals, int nout_als, int out_als);
 
diff --git a/ccall.c b/ccall.c
index 561b2e4..bb43d61 100644
--- a/ccall.c
+++ b/ccall.c
@@ -232,11 +232,10 @@ static int update_bcf1(call_t *call, bcf1_t *rec, const bcf_p1rst_t *pr, double
 
     // Remove unused alleles
     int nals_ori = rec->n_allele, nals = !is_var && !(call->flag & CALL_KEEPALT) ? 1 : pr->rank0 < 2? 2 : pr->rank0+1;
-    if ( call->flag & CALL_KEEPALT && nals>1 )
+    if ( call->flag & CALL_KEEPALT && call->unseen>0 )
     {
-        if ( rec->d.allele[nals-1][0]=='X' ) nals--;   // old version of unseen allele "X"
-        else if ( rec->d.allele[nals-1][0]=='<' && rec->d.allele[nals-1][1]=='X' && rec->d.allele[nals-1][2]=='>' ) nals--;   // old version of unseen allele, "<X>"
-        else if ( rec->d.allele[nals-1][0]=='<' && rec->d.allele[nals-1][1]=='*' && rec->d.allele[nals-1][2]=='>' ) nals--;   // new version of unseen allele, "<*>"
+        assert( call->unseen==nals-1 );
+        nals--;
     }
     
     if ( nals<rec->n_allele )
diff --git a/consensus.c b/consensus.c
index 08f3d7d..7a615fe 100644
--- a/consensus.c
+++ b/consensus.c
@@ -26,6 +26,8 @@
 
 #include <stdio.h>
 #include <stdlib.h>
+#include <string.h>
+#include <errno.h>
 #include <getopt.h>
 #include <unistd.h>
 #include <ctype.h>
@@ -205,11 +207,16 @@ static void init_data(args_t *args)
     if ( args->chain_fname )
     {
         args->fp_chain = fopen(args->chain_fname,"w");
+        if ( ! args->fp_chain ) error("Failed to create %s: %s\n", args->chain_fname, strerror(errno));
         args->chain_id = 0;
     }
     rbuf_init(&args->vcf_rbuf, 100);
     args->vcf_buf = (bcf1_t**) calloc(args->vcf_rbuf.m, sizeof(bcf1_t*));
-    args->fp_out = args->output_fname ? fopen(args->output_fname,"w") : stdout;
+    if ( args->output_fname ) {
+        args->fp_out = fopen(args->output_fname,"w");
+        if ( ! args->fp_out ) error("Failed to create %s: %s\n", args->output_fname, strerror(errno));
+    }
+    else args->fp_out = stdout;
 }
 
 static void destroy_data(args_t *args)
@@ -560,7 +567,7 @@ static void consensus(args_t *args)
             }
 
             // is the cached fasta buffer full enough? if not, read more fasta, no flushing
-            if ( args->fa_ori_pos + args->fa_buf.l - args->fa_mod_off <= rec->pos + rec->rlen )
+            if ( args->fa_ori_pos + args->fa_buf.l - args->fa_mod_off < rec->pos + rec->rlen )
             {
                 unread_vcf_line(args, rec_ptr);
                 break;
diff --git a/convert.c b/convert.c
index f3999ab..3e289f0 100644
--- a/convert.c
+++ b/convert.c
@@ -84,6 +84,8 @@ struct _convert_t
     int nreaders;
     void *dat;
     int ndat;
+    char *undef_info_tag;
+    int allow_undef_tags;
 };
 
 
@@ -138,14 +140,32 @@ static void process_filter(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isa
     }
     else kputc('.', str);
 }
-static inline int bcf_array_ivalue(void *bcf_array, int type, int idx)
+static inline int32_t bcf_array_ivalue(void *bcf_array, int type, int idx)
 {
-    if ( type==BCF_BT_INT8 ) return ((int8_t*)bcf_array)[idx];
-    if ( type==BCF_BT_INT16 ) return ((int16_t*)bcf_array)[idx];
+    if ( type==BCF_BT_INT8 )
+    {
+        int8_t val = ((int8_t*)bcf_array)[idx];
+        if ( val==bcf_int8_missing ) return bcf_int32_missing;
+        if ( val==bcf_int8_vector_end ) return bcf_int32_vector_end;
+        return val;
+    }
+    if ( type==BCF_BT_INT16 )
+    {
+        int16_t val = ((int16_t*)bcf_array)[idx];
+        if ( val==bcf_int16_missing ) return bcf_int32_missing;
+        if ( val==bcf_int16_vector_end ) return bcf_int32_vector_end;
+        return val;
+    }
     return ((int32_t*)bcf_array)[idx];
 }
 static void process_info(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str)
 {
+    if ( fmt->id<0 )
+    {
+        kputc('.', str);
+        return;
+    }
+
     int i;
     for (i=0; i<line->n_info; i++)
         if ( line->d.info[i].key == fmt->id ) break;
@@ -206,11 +226,16 @@ static void process_info(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isamp
 static void init_format(convert_t *convert, bcf1_t *line, fmt_t *fmt)
 {
     fmt->id = bcf_hdr_id2int(convert->header, BCF_DT_ID, fmt->key);
-    if ( fmt->id==-1 ) error("Error: no such tag defined in the VCF header: FORMAT/%s\n", fmt->key);
     fmt->fmt = NULL;
-    int i;
-    for (i=0; i<(int)line->n_fmt; i++)
-        if ( line->d.fmt[i].id==fmt->id ) { fmt->fmt = &line->d.fmt[i]; break; }
+    if ( fmt->id >= 0 )
+    {
+        int i;
+        for (i=0; i<(int)line->n_fmt; i++)
+            if ( line->d.fmt[i].id==fmt->id ) { fmt->fmt = &line->d.fmt[i]; break; }
+    }
+    else if ( !convert->allow_undef_tags )
+        error("Error: no such tag defined in the VCF header: FORMAT/%s\n", fmt->key);
+
     fmt->ready = 1;
 }
 static void process_format(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str)
@@ -230,8 +255,22 @@ static void process_format(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isa
             kputc('.', str);
             return;
         }
-        if ( fmt->fmt->type == BCF_BT_FLOAT ) ksprintf(str, "%g", ((float*)(fmt->fmt->p + isample*fmt->fmt->size))[fmt->subscript]);
-        else if ( fmt->fmt->type != BCF_BT_CHAR ) kputw(bcf_array_ivalue(fmt->fmt->p+isample*fmt->fmt->size,fmt->fmt->type,fmt->subscript), str);
+        if ( fmt->fmt->type == BCF_BT_FLOAT )
+        {
+            float *ptr = (float*)(fmt->fmt->p + isample*fmt->fmt->size);
+            if ( bcf_float_is_missing(ptr[fmt->subscript]) || bcf_float_is_vector_end(ptr[fmt->subscript]) )
+                kputc('.', str);
+            else
+                ksprintf(str, "%g", ptr[fmt->subscript]);
+        }
+        else if ( fmt->fmt->type != BCF_BT_CHAR )
+        {
+            int32_t ival = bcf_array_ivalue(fmt->fmt->p+isample*fmt->fmt->size,fmt->fmt->type,fmt->subscript);
+            if ( ival==bcf_int32_missing || ival==bcf_int32_vector_end )
+                kputc('.', str);
+            else
+                kputw(ival, str);
+        }
         else error("TODO: %s:%d .. fmt->type=%d\n", __FILE__,__LINE__, fmt->fmt->type);
     }
     else
@@ -419,7 +458,9 @@ static void process_gt_to_prob3(convert_t *convert, bcf1_t *line, fmt_t *fmt, in
         if ( j==2 )
         {
             // diploid
-            if ( bcf_gt_allele(ptr[0])!=bcf_gt_allele(ptr[1]) )
+            if ( bcf_gt_is_missing(ptr[0]) )
+                kputs(" 0.33 0.33 0.33", str);
+            else if ( bcf_gt_allele(ptr[0])!=bcf_gt_allele(ptr[1]) )
                 kputs(" 0 1 0", str);       // HET
             else if ( bcf_gt_allele(ptr[0])==1 )
                 kputs(" 0 0 1", str);       // ALT HOM, first ALT allele
@@ -726,7 +767,7 @@ static fmt_t *register_tag(convert_t *convert, int type, char *key, int is_gtf)
         if ( fmt->type==T_INFO )
         {
             fmt->id = bcf_hdr_id2int(convert->header, BCF_DT_ID, key);
-            if ( fmt->id==-1 ) error("Error: no such tag defined in the VCF header: INFO/%s\n", key);
+            if ( fmt->id==-1 ) convert->undef_info_tag = strdup(key);
         }
     }
     return fmt;
@@ -757,6 +798,17 @@ static char *parse_tag(convert_t *convert, char *p, int is_gtf)
         else if ( !strcmp(str.s, "GT") ) register_tag(convert, T_GT, "GT", is_gtf);
         else if ( !strcmp(str.s, "TGT") ) register_tag(convert, T_TGT, "GT", is_gtf);
         else if ( !strcmp(str.s, "IUPACGT") ) register_tag(convert, T_IUPAC_GT, "GT", is_gtf);
+        else if ( !strcmp(str.s, "INFO") )
+        {
+            if ( *q!='/' ) error("Could not parse format string: %s\n", convert->format_str);
+            p = ++q;
+            str.l = 0;
+            while ( *q && (isalnum(*q) || *q=='_' || *q=='.') ) q++;
+            if ( q-p==0 ) error("Could not parse format string: %s\n", convert->format_str);
+            kputsn(p, q-p, &str);
+            fmt_t *fmt = register_tag(convert, T_INFO, str.s, is_gtf);
+            fmt->subscript = parse_subscript(&q);
+        }
         else
         {
             fmt_t *fmt = register_tag(convert, T_FORMAT, str.s, is_gtf);
@@ -836,6 +888,7 @@ convert_t *convert_init(bcf_hdr_t *hdr, int *samples, int nsamples, const char *
     convert_t *convert = (convert_t*) calloc(1,sizeof(convert_t));
     convert->header = hdr;
     convert->format_str = strdup(format_str);
+    convert->max_unpack = BCF_UN_STR;
 
     int i, is_gtf = 0;
     char *p = convert->format_str;
@@ -870,8 +923,9 @@ void convert_destroy(convert_t *convert)
 {
     int i;
     for (i=0; i<convert->nfmt; i++)
-        if ( convert->fmt[i].key ) free(convert->fmt[i].key);
-    if ( convert->mfmt ) free(convert->fmt);
+        free(convert->fmt[i].key);
+    free(convert->fmt);
+    free(convert->undef_info_tag);
     free(convert->dat);
     free(convert->samples);
     free(convert->format_str);
@@ -929,6 +983,9 @@ int convert_header(convert_t *convert, kstring_t *str)
 
 int convert_line(convert_t *convert, bcf1_t *line, kstring_t *str)
 {
+    if ( !convert->allow_undef_tags && convert->undef_info_tag )
+        error("Error: no such tag defined in the VCF header: INFO/%s\n", convert->undef_info_tag);
+
     int l_ori = str->l;
     bcf_unpack(line, convert->max_unpack);
 
@@ -974,3 +1031,26 @@ int convert_line(convert_t *convert, bcf1_t *line, kstring_t *str)
     return str->l - l_ori;
 }
 
+int convert_set_option(convert_t *convert, enum convert_option opt, ...)
+{
+    int ret = 0;
+    va_list args;
+
+    va_start(args, opt);
+    switch (opt) 
+    {
+        case allow_undef_tags:
+            convert->allow_undef_tags = va_arg(args, int);
+            break;
+        default:
+            ret = -1;
+    }
+    va_end(args);
+    return ret;
+}
+
+int convert_max_unpack(convert_t *convert)
+{
+    return convert->max_unpack;
+}
+
diff --git a/convert.h b/convert.h
index 72e375c..3712338 100644
--- a/convert.h
+++ b/convert.h
@@ -28,11 +28,17 @@ THE SOFTWARE.  */
 #include <htslib/vcf.h>
 
 typedef struct _convert_t convert_t;
+enum convert_option
+{
+    allow_undef_tags
+};
 
 convert_t *convert_init(bcf_hdr_t *hdr, int *samples, int nsamples, const char *str);
 void convert_destroy(convert_t *convert);
+int convert_set_option(convert_t *convert, enum convert_option opt, ...);
 int convert_header(convert_t *convert, kstring_t *str);
 int convert_line(convert_t *convert, bcf1_t *rec, kstring_t *str);
+int convert_max_unpack(convert_t *convert);
 
 #endif
 
diff --git a/doc/bcftools.1 b/doc/bcftools.1
index dc03dc6..d2783d4 100644
--- a/doc/bcftools.1
+++ b/doc/bcftools.1
@@ -2,12 +2,12 @@
 .\"     Title: bcftools
 .\"    Author: [see the "AUTHORS" section]
 .\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\"      Date: 2015-01-21 15:01 GMT
+.\"      Date: 2015-12-15 14:02 GMT
 .\"    Manual: \ \&
 .\"    Source: \ \&
 .\"  Language: English
 .\"
-.TH "BCFTOOLS" "1" "2015\-01\-21 15:01 GMT" "\ \&" "\ \&"
+.TH "BCFTOOLS" "1" "2015\-12\-15 14:02 GMT" "\ \&" "\ \&"
 .\" -----------------------------------------------------------------
 .\" * Define some portability stuff
 .\" -----------------------------------------------------------------
@@ -31,17 +31,17 @@
 bcftools \- utilities for variant calling and manipulating VCFs and BCFs\&.
 .SH "SYNOPSIS"
 .sp
-\fBbcftools\fR [\fICOMMAND\fR] [\fIOPTIONS\fR]
+\fBbcftools\fR [\-\-version|\-\-version\-only] [\-\-help] [\fICOMMAND\fR] [\fIOPTIONS\fR]
 .SH "DESCRIPTION"
 .sp
 BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF\&. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF\-compressed\&.
 .sp
-Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically even when streaming from a pipe\&. Indexed VCF and BCF will work in all situations\&. Un\-indexed VCF and BCF and streams will work in most, but not all situations\&.
+Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically even when streaming from a pipe\&. Indexed VCF and BCF will work in all situations\&. Un\-indexed VCF and BCF and streams will work in most, but not all situations\&. In general, whenever multiple VCFs are read simultaneously, they must be indexed and therefore also compressed\&.
 .sp
 BCFtools is designed to work on a stream\&. It regards an input file "\-" as the standard input (stdin) and outputs to the standard output (stdout)\&. Several commands can thus be combined with Unix pipes\&.
 .SS "VERSION"
 .sp
-This manual page was last updated \fB2015\-01\-21 15:01 GMT\fR and refers to bcftools git version \fB1\&.1\-140\-g9b0e7cc+\fR\&.
+This manual page was last updated \fB2015\-12\-15 14:02 GMT\fR and refers to bcftools git version \fB1\&.2\-191\-g6737c5c+\fR\&.
 .SS "BCF1"
 .sp
 The BCF1 format output by versions of samtools <= 0\&.1\&.19 is \fBnot\fR compatible with this version of bcftools\&. To read BCF1 files one can use the view command from old versions of bcftools packaged with samtools versions <= 0\&.1\&.19 to convert to VCF, which can then be read by this version of bcftools\&.
@@ -97,6 +97,19 @@ For a full list of available commands, run \fBbcftools\fR without arguments\&. F
 .IP \(bu 2.3
 .\}
 
+\fBcnv\fR
+\&.\&. Copy Number Variation caller
+.RE
+.sp
+.RS 4
+.ie n \{\
+\h'-04'\(bu\h'+03'\c
+.\}
+.el \{\
+.sp -1
+.IP \(bu 2.3
+.\}
+
 \fBconcat\fR
 \&.\&. concatenate VCF/BCF files from the same set of samples
 .RE
@@ -227,6 +240,19 @@ For a full list of available commands, run \fBbcftools\fR without arguments\&. F
 .IP \(bu 2.3
 .\}
 
+\fBpolysomy\fR
+\&.\&. detect contaminations and whole\-chromosome aberrations
+.RE
+.sp
+.RS 4
+.ie n \{\
+\h'-04'\(bu\h'+03'\c
+.\}
+.el \{\
+.sp -1
+.IP \(bu 2.3
+.\}
+
 \fBquery\fR
 \&.\&. transform VCF/BCF into user\-defined formats
 .RE
@@ -376,7 +402,7 @@ rather than to standard output, where it is written by default\&.
 .PP
 \fB\-O, \-\-output\-type\fR \fIb\fR|\fIu\fR|\fIz\fR|\fIv\fR
 .RS 4
-Output compressed BCF (\fIb\fR), uncompressed BCF (\fIu\fR), compressed VCF (\fIz\fR), uncompressed VCF (\fIv\fR)\&.
+Output compressed BCF (\fIb\fR), uncompressed BCF (\fIu\fR), compressed VCF (\fIz\fR), uncompressed VCF (\fIv\fR)\&. Use the \-Ou option when piping between bcftools subcommands to speed up performance by removing unecessary compression/decompression and VCF←→BCF conversion\&.
 .RE
 .PP
 \fB\-r, \-\-regions\fR \fIchr\fR|\fIchr:pos\fR|\fIchr:from\-to\fR|\fIchr:from\-\fR[,\&...]
@@ -404,17 +430,62 @@ cannot be used in combination with
 .PP
 \fB\-s, \-\-samples\fR [^]\fILIST\fR
 .RS 4
-Comma\-separated list of samples to include or exclude if prefixed with "^"\&.
+Comma\-separated list of samples to include or exclude if prefixed with "^"\&. Note that in general tags such as INFO/AC, INFO/AN, etc are not updated to correspond to the subset samples\&.
+\fBbcftools view\fR
+is the exception where some tags will be updated (unless the
+\fB\-I, \-\-no\-update\fR
+option is used; see
+\fBbcftools view\fR
+documentation)\&. To use updated tags for the subset in another command one can pipe from
+\fBview\fR
+into that command\&. For example:
 .RE
+.sp
+.if n \{\
+.RS 4
+.\}
+.nf
+    bcftools view \-Ou \-s sample1,sample2 file\&.vcf | bcftools query \-f %INFO/AC\et%INFO/AN\en
+.fi
+.if n \{\
+.RE
+.\}
 .PP
 \fB\-S, \-\-samples\-file\fR \fIFILE\fR
 .RS 4
-File of sample names to include or exclude if prefixed with "^"\&. One sample per line\&. The command
+File of sample names to include or exclude if prefixed with "^"\&. One sample per line\&. See also the note above for the
+\fB\-s, \-\-samples\fR
+option\&. The command
 \fBbcftools call\fR
-accepts an optional second column indicating ploidy (0, 1 or 2) and can parse also PED files\&. With
+accepts an optional second column indicating ploidy (0, 1 or 2) or sex (as defined by
+\fB\-\-ploidy\fR, for example "F" or "M"), and can parse also PED files\&. If the second column is not present, the sex "F" is assumed\&. With
 \fBbcftools call\fR\fB \-C\fR
-\fItrio\fR, PED file is expected\&.
+\fItrio\fR, PED file is expected\&. File formats examples:
+.RE
+.sp
+.if n \{\
+.RS 4
+.\}
+.nf
+    sample1    1
+    sample2    2
+    sample3    2
+
+  or
+
+    sample1    M
+    sample2    F
+    sample3    F
+
+  or a \&.ped file (here is shown a minimum working example, the first column is
+  ignored and the last indicates sex: 1=male, 2=female)
+
+    ignored daughterA fatherA motherA 2
+    ignored sonB fatherB motherB 1
+.fi
+.if n \{\
 .RE
+.\}
 .PP
 \fB\-t, \-\-targets\fR [^]\fIchr\fR|\fIchr:pos\fR|\fIchr:from\-to\fR|\fIchr:from\-\fR[,\&...]
 .RS 4
@@ -451,18 +522,28 @@ cannot be used in combination with
 With the
 \fBcall \-C\fR
 \fIalleles\fR
-command, third column of the targets file must be comma\-separated list of alleles, starting with the reference allele\&. Such a file can be easily created from a VCF using:
+command, third column of the targets file must be comma\-separated list of alleles, starting with the reference allele\&. Note that the file must be compressed and index\&. Such a file can be easily created from a VCF using:
 .RE
 .sp
 .if n \{\
 .RS 4
 .\}
 .nf
-    bcftools query \-f\*(Aq%CHROM\et%POS\et%REF,%ALT\en\*(Aq file\&.vcf
+    bcftools query \-f\*(Aq%CHROM\et%POS\et%REF,%ALT\en\*(Aq file\&.vcf | bgzip \-c > als\&.tsv\&.gz && tabix \-s1 \-b2 \-e2 als\&.tsv\&.gz
 .fi
 .if n \{\
 .RE
 .\}
+.PP
+\fB\-\-threads\fR \fIINT\fR
+.RS 4
+Number of output compression threads to use in addition to main thread\&. Only used when
+\fI\-\-output\-type\fR
+is
+\fIb\fR
+or
+\fIz\fR\&. Default: 0\&.
+.RE
 .SS "bcftools annotate \fI[OPTIONS]\fR \fIFILE\fR"
 .sp
 This command allows to add or remove annotations\&.
@@ -493,7 +574,7 @@ and
 Comma\-separated list of columns or tags to carry over from the annotation file (see also
 \fB\-a, \-\-annotations\fR)\&. If the annotation file is not a VCF/BCF,
 \fIlist\fR
-describes the columns of the annotation file and must include CHROM, POS (or, alternatively, FROM and TO), and optionally REF and ALT\&. Unused columns which should be ignored can be indicated by "\-"\&. If the annotation file is a VCF/BCF, only the edited columns/tags must be present and their order does not matter\&. The columns ID, QUAL, FILTER, INFO and FORMAT can be edited, where INFO tags can be written both as "INFO/TAG" or simply "TAG", and FORMAT tags can be written as "FORMAT/T [...]
+describes the columns of the annotation file and must include CHROM, POS (or, alternatively, FROM and TO), and optionally REF and ALT\&. Unused columns which should be ignored can be indicated by "\-"\&. If the annotation file is a VCF/BCF, only the edited columns/tags must be present and their order does not matter\&. The columns ID, QUAL, FILTER, INFO and FORMAT can be edited, where INFO tags can be written both as "INFO/TAG" or simply "TAG", and FORMAT tags can be written as "FORMAT/T [...]
 \fB\-h, \-\-header\-lines\fR\&.
 .RE
 .PP
@@ -549,6 +630,13 @@ is true\&. For valid expressions see
 \fBEXPRESSIONS\fR\&.
 .RE
 .PP
+\fB\-m, \-\-mark\-sites\fR \fITAG\fR
+.RS 4
+annotate sites which are present ("+") or absent ("\-") in the
+\fB\-a\fR
+file with a new INFO/TAG flag
+.RE
+.PP
 \fB\-o, \-\-output\fR \fIFILE\fR
 .RS 4
 see
@@ -592,6 +680,12 @@ subset of samples to annotate\&. If the samples are named differently in the tar
 VCF, the name mapping can be given as "src_name dst_name\en", separated by whitespaces, each pair on a separate line\&.
 .RE
 .PP
+\fB\-\-threads\fR \fIINT\fR
+.RS 4
+see
+\fBCommon Options\fR
+.RE
+.PP
 \fB\-x, \-\-remove\fR \fIlist\fR
 .RS 4
 List of annotations to remove\&. Use "FILTER" to remove all filters or "FILTER/SomeFilter" to remove a specific filter\&. Similarly, "INFO" can be used to remove all INFO tags and "FORMAT" to remove all FORMAT tags except GT\&. To remove all INFO tags except "FOO" and "BAR", use "^INFO/FOO,INFO/BAR" (and similarly for FORMAT and FILTER)\&. "INFO" can be abbreviated to "INF" and "FORMAT" to "FMT"\&.
@@ -630,6 +724,131 @@ List of annotations to remove\&. Use "FILTER" to remove all filters or "FILTER/S
 .if n \{\
 .RE
 .\}
+.SS "bcftools cnv \fI[OPTIONS]\fR \fIFILE\fR"
+.sp
+Copy number variation caller, requires a VCF annotated with the Illumina\(cqs B\-allele frequency (BAF) and Log R Ratio intensity (LRR) values\&. The HMM considers the following copy number states: CN 2 (normal), 1 (single\-copy loss), 0 (complete loss), 3 (single\-copy gain)\&.
+.sp
+.it 1 an-trap
+.nr an-no-space-flag 1
+.nr an-break-flag 1
+.br
+.ps +1
+\fBGeneral Options:\fR
+.RS 4
+.PP
+\fB\-c, \-\-control\-sample\fR \fIstring\fR
+.RS 4
+optional control sample name\&. If given, pairwise calling is performed and the
+\fB\-P\fR
+option can be used
+.RE
+.PP
+\fB\-f, \-\-AF\-file\fR \fIfile\fR
+.RS 4
+read allele frequencies from a tab\-delimited file with the columns CHR,POS,REF,ALT,AF
+.RE
+.PP
+*\-o, \-\-output\-dir \fIpath\fR
+.RS 4
+output directory
+.RE
+.PP
+*\-p, \-\-plot\-threshold \fIfloat\fR
+.RS 4
+call
+\fBmatplotlib\fR
+to produce plots for chromosomes with quality at least
+\fIfloat\fR, useful for visual inspection of the calls\&. With
+\fB\-p 0\fR, plots for all chromosomes will be generated\&. If not given, a
+\fBmatplotlib\fR
+script will be created but not called\&.
+.RE
+.PP
+\fB\-r, \-\-regions\fR \fIchr\fR|\fIchr:pos\fR|\fIchr:from\-to\fR|\fIchr:from\-\fR[,\&...]
+.RS 4
+see
+\fBCommon Options\fR
+.RE
+.PP
+\fB\-R, \-\-regions\-file\fR \fIfile\fR
+.RS 4
+see
+\fBCommon Options\fR
+.RE
+.PP
+\fB\-s, \-\-query\-sample\fR \fIstring\fR
+.RS 4
+query samply name
+.RE
+.PP
+\fB\-t, \-\-targets\fR \fILIST\fR
+.RS 4
+see
+\fBCommon Options\fR
+.RE
+.PP
+\fB\-T, \-\-targets\-file\fR \fIFILE\fR
+.RS 4
+see
+\fBCommon Options\fR
+.RE
+.RE
+.sp
+.it 1 an-trap
+.nr an-no-space-flag 1
+.nr an-break-flag 1
+.br
+.ps +1
+\fBHMM Options:\fR
+.RS 4
+.PP
+\fB\-a, \-\-aberrant\fR \fIfloat\fR[,\fIfloat\fR]
+.RS 4
+fraction of aberrant cells in query and control\&. The hallmark of duplications and contaminations is the BAF value of heterozygous markers which is dependent on the fraction of aberrant cells\&. Sensitivity to smaller fractions of cells can be increased by setting
+\fB\-a\fR
+to a lower value\&. Note however, that this comes at the cost of increased false discovery rate\&.
+.RE
+.PP
+\fB\-b, \-\-BAF\-weight\fR \fIfloat\fR
+.RS 4
+relative contribution from BAF
+.RE
+.PP
+\fBd, \-\-BAF\-dev\fR \fIfloat\fR[,\fIfloat\fR]
+.RS 4
+expected BAF deviation in query and control, i\&.e\&. the noise observed in the data\&.
+.RE
+.PP
+\fB\-e, \-\-err\-prob\fR \fIfloat\fR
+.RS 4
+uniform error probability
+.RE
+.PP
+\fB\-l, \-\-LRR\-weight\fR \fIfloat\fR
+.RS 4
+relative contribution from LRR\&. With noisy data, this option can have big effect on the number of calls produced\&. In truly random noise (such as in simulated data), the value should be set high (1\&.0), but in the presence of systematic noise when LRR are not informative, lower values result in cleaner calls (0\&.2)\&.
+.RE
+.PP
+\fB\-L, \-\-LRR\-smooth\-win\fR \fIint\fR
+.RS 4
+reduce LRR noise by applying moving average given this window size
+.RE
+.PP
+\fB\-O, \-\-optimize\fR \fIfloat\fR
+.RS 4
+iteratively estimate the fraction of aberrant cells, down to the given fraction\&. Lowering this value from the default 1\&.0 to say, 0\&.3, can help discover more events but also increases noise
+.RE
+.PP
+\fB\-P, \-\-same\-prob\fR \fIfloat\fR
+.RS 4
+the prior probability of the query and the control sample being the same\&. Setting to 0 calls both independently, setting to 1 forces the same copy number state in both\&.
+.RE
+.PP
+\fB\-x, \-\-xy\-prob\fR \fIfloat\fR
+.RS 4
+the HMM probability of transition to another copy number state\&. Increasing this values leads to smaller and more frequent calls\&.
+.RE
+.RE
 .SS "bcftools call \fI[OPTIONS]\fR \fIFILE\fR"
 .sp
 This command replaces the former \fBbcftools view\fR caller\&. Some of the original functionality has been temporarily lost in the process of transition under htslib, but will be added back on popular demand\&. The original calling model can be invoked with the \fB\-c\fR option\&.
@@ -642,12 +861,49 @@ This command replaces the former \fBbcftools view\fR caller\&. Some of the origi
 \fBFile format options:\fR
 .RS 4
 .PP
+\fB\-o, \-\-output\fR \fIFILE\fR
+.RS 4
+see
+\fBCommon Options\fR
+.RE
+.PP
 \fB\-O, \-\-output\-type\fR \fIb\fR|\fIu\fR|\fIz\fR|\fIv\fR
 .RS 4
 see
 \fBCommon Options\fR
 .RE
 .PP
+\fB\-\-ploidy\fR \fIASSEMBLY\fR[\fI?\fR]
+.RS 4
+predefined ploidy, use
+\fIlist\fR
+(or any other unused word) to print a list of all predefined assemblies\&. Append a question mark to print the actual definition\&. See also
+\fB\-\-ploidy\-file\fR\&.
+.RE
+.PP
+\fB\-\-ploidy\-file\fR \fIFILE\fR
+.RS 4
+ploidy definition given as a space/tab\-delimited list of CHROM, FROM, TO, SEX, PLOIDY\&. The SEX codes are arbitrary and correspond to the ones used by
+\fB\-\-samples\-file\fR\&. The default ploidy can be given using the starred records (see below), unlisted regions have ploidy 2\&. The default ploidy definition is
+.RE
+.sp
+.if n \{\
+.RS 4
+.\}
+.nf
+    X 1 60000 M 1
+    X 2699521 154931043 M 1
+    Y 1 59373566 M 1
+    Y 1 59373566 F 0
+    MT 1 16569 M 1
+    MT 1 16569 F 1
+    *  * *     M 2
+    *  * *     F 2
+.fi
+.if n \{\
+.RE
+.\}
+.PP
 \fB\-r, \-\-regions\fR \fIchr\fR|\fIchr:pos\fR|\fIchr:from\-to\fR|\fIchr:from\-\fR[,\&...]
 .RS 4
 see
@@ -683,6 +939,12 @@ see
 see
 \fBCommon Options\fR
 .RE
+.PP
+\fB\-\-threads\fR \fIINT\fR
+.RS 4
+see
+\fBCommon Options\fR
+.RE
 .RE
 .sp
 .it 1 an-trap
@@ -710,15 +972,15 @@ output also gVCF blocks of homozygous REF calls\&. The parameter
 is the minimum per\-sample depth required to include a site in the non\-variant block\&.
 .RE
 .PP
-\fB\-M, \-\-keep\-masked\-ref\fR
+\fB\-i, \-\-insert\-missed\fR \fIINT\fR
 .RS 4
-output sites where REF allele is N
+output also sites missed by mpileup but present in
+\fB\-T, \-\-targets\-file\fR\&.
 .RE
 .PP
-\fB\-o, \-\-output\fR \fIFILE\fR
+\fB\-M, \-\-keep\-masked\-ref\fR
 .RS 4
-see
-\fBCommon Options\fR
+output sites where REF allele is N
 .RE
 .PP
 \fB\-V, \-\-skip\-variants\fR \fIsnps\fR|\fIindels\fR
@@ -821,12 +1083,23 @@ Concatenate or combine VCF/BCF files\&. All source files must have the same samp
 First coordinate of the next file can precede last record of the current file\&.
 .RE
 .PP
-\fB\-D, \-\-remove\-duplicates\fR
+\fB\-c, \-\-compact\-PS\fR
+.RS 4
+Do not output PS tag at each site, only at the start of a new phase set block\&.
+.RE
+.PP
+\fB\-d, \-\-rm\-dups\fR \fIsnps\fR|\fIindels\fR|\fIboth\fR|\fIall\fR|\fInone\fR
 .RS 4
-If a record is present in multiple files, output only the first instance\&. Requires
+Output duplicate records of specified type present in multiple files only once\&. Requires
 \fB\-a, \-\-allow\-overlaps\fR\&.
 .RE
 .PP
+\fB\-D, \-\-remove\-duplicates\fR
+.RS 4
+Alias for
+\fB\-d none\fR
+.RE
+.PP
 \fB\-f, \-\-file\-list\fR \fIFILE\fR
 .RS 4
 Read the list of files from a file\&.
@@ -868,6 +1141,12 @@ see
 \fBCommon Options\fR\&. Requires
 \fB\-a, \-\-allow\-overlaps\fR\&.
 .RE
+.PP
+\fB\-\-threads\fR \fIINT\fR
+.RS 4
+see
+\fBCommon Options\fR
+.RE
 .SS "bcftools consensus \fI[OPTIONS]\fR \fIFILE\fR"
 .sp
 Create consensus sequence by applying VCF variants to a reference fasta file\&.
@@ -1005,6 +1284,12 @@ see
 see
 \fBCommon Options\fR
 .RE
+.PP
+\fB\-\-threads\fR \fIINT\fR
+.RS 4
+see
+\fBCommon Options\fR
+.RE
 .RE
 .sp
 .it 1 an-trap
@@ -1065,6 +1350,11 @@ tag to take values for \&.gen file: GT,PL,GL,GP
 .RS 4
 convert gVCF to VCF, expanding REF blocks into sites\&. Only sites with FILTER set to "PASS" or "\&." will be expanded\&.
 .RE
+.PP
+\fB\-f, \-\-fasta\-ref\fR \fIfile\fR
+.RS 4
+reference sequence in fasta format\&. Must be indexed with samtools faidx
+.RE
 .RE
 .sp
 .it 1 an-trap
@@ -1077,7 +1367,7 @@ convert gVCF to VCF, expanding REF blocks into sites\&. Only sites with FILTER s
 .PP
 \fB\-\-hapsample2vcf\fR \fIprefix\fR or \fIhaps\-file\fR,\fIsample\-file\fR
 .RS 4
-convert from haps/sample format to VCF\&. The columns of \&.haps file are similar to \&.gen file above, but there are only two haplotype columns per sample\&. Note that the first column of the haps file is expected to be in the form "CHR:POS_REF_ALT", for example:
+convert from haps/sample format to VCF\&. The columns of \&.haps file are similar to \&.gen file above, but there are only two haplotype columns per sample\&. Note that the first column of the haps file is expected to be in the form "CHR:POS_REF_ALT(_END)?", with the _END being optional for defining the INFO/END tag when ALT is a symbolic allele, for example:
 .RE
 .sp
 .if n \{\
@@ -1088,10 +1378,31 @@ convert from haps/sample format to VCF\&. The columns of \&.haps file are simila
   \-\-\-\-
   1:111485207_G_A rsID1 111485207 G A 0 1 0 0
   1:111494194_C_T rsID2 111494194 C T 0 1 0 0
+  1:111495231_A_<DEL>_111495784 rsID3 111495231 A <DEL> 0 0 1 0
 .fi
 .if n \{\
 .RE
 .\}
+.PP
+\fB\-\-hapsample\fR \fIprefix\fR or \fIhaps\-file\fR,\fIsample\-file\fR
+.RS 4
+convert from VCF to haps/sample format used by IMPUTE2 and SHAPEIT\&. The columns of \&.haps file begin with ID,RSID,POS,REF,ALT\&. In order to prevent strand swaps, the program uses IDs of the form "CHROM:POS_REF_ALT"\&.
+.RE
+.PP
+\fB\-\-haploid2diploid\fR
+.RS 4
+with
+\fB\-h\fR
+option converts haploid genotypes to homozygous diploid genotypes\&. For example, the program will print
+\fI0 0\fR
+instead of the default
+\fI0 \-\fR\&. This is useful for programs which do not handle haploid genotypes correctly\&.
+.RE
+.PP
+\fB\-\-vcf\-ids\fR
+.RS 4
+output VCF IDs instead of "CHROM:POS_REF_ALT" IDs
+.RE
 .RE
 .sp
 .it 1 an-trap
@@ -1175,7 +1486,7 @@ comma\-separated list of fields in the input file\&. In the current version, the
 .PP
 \fB\-f, \-\-fasta\-ref\fR \fIfile\fR
 .RS 4
-reference sequence in fasta format
+reference sequence in fasta format\&. Must be indexed with samtools faidx
 .RE
 .PP
 \fB\-s, \-\-samples\fR \fILIST\fR
@@ -1556,9 +1867,9 @@ is true\&. See discussion of
 above\&.
 .RE
 .PP
-\fB\-n, \-\-nfiles\fR [+\-=]\fIINT\fR
+\fB\-n, \-\-nfiles\fR [+\-=]\fIINT\fR|~\fIBITMAP\fR
 .RS 4
-output positions present in this many (=), this many or more (+), or this many or fewer (\-) files
+output positions present in this many (=), this many or more (+), this many or fewer (\-), or the exact same (~) files
 .RE
 .PP
 \fB\-o, \-\-output\fR \fIFILE\fR
@@ -1668,6 +1979,18 @@ Extract records private to A or B comparing by position only
 .if n \{\
 .RE
 .\}
+.sp
+Print a list of records which are present in A and B but not in C and D
+.sp
+.if n \{\
+.RS 4
+.\}
+.nf
+    bcftools isec \-n~1100 \-c all A\&.vcf\&.gz B\&.vcf\&.gz C\&.vcf\&.gz D\&.vcf\&.gz
+.fi
+.if n \{\
+.RE
+.\}
 .RE
 .SS "bcftools merge [\fIOPTIONS\fR] \fIA\&.vcf\&.gz\fR \fIB\&.vcf\&.gz\fR [\&...]"
 .sp
@@ -1712,7 +2035,9 @@ is one of
 \fIavg\fR,
 \fImin\fR,
 \fImax\fR,
-\fIjoin\fR\&.
+\fIjoin\fR\&. Default is
+\fIDP:sum,DP4:sum\fR
+if these fields exist in the input files\&. Fields with no specified rule will take the value from the first input file\&. The merged QUAL value is currently set to the maximum\&. This behaviour is not user controllable at the moment\&.
 .RE
 .PP
 \fB\-l, \-\-file\-list\fR \fIFILE\fR
@@ -1764,18 +2089,49 @@ see
 see
 \fBCommon Options\fR
 .RE
+.PP
+\fB\-\-threads\fR \fIINT\fR
+.RS 4
+see
+\fBCommon Options\fR
+.RE
 .SS "bcftools norm [\fIOPTIONS\fR] \fIfile\&.vcf\&.gz\fR"
 .sp
-Left\-align and normalize indels, check if REF alleles match the reference, split multiallelic sites into multiple rows; recover multiallelics from multiple rows\&.
+Left\-align and normalize indels, check if REF alleles match the reference, split multiallelic sites into multiple rows; recover multiallelics from multiple rows\&. Left\-alignment and normalization will only be applied if the \fB\-\-fasta\-ref\fR option is supplied\&.
+.PP
+\fB\-c, \-\-check\-ref\fR \fIe\fR|\fIw\fR|\fIx\fR|\fIs\fR
+.RS 4
+what to do when incorrect or missing REF allele is encountered: exit (\fIe\fR), warn (\fIw\fR), exclude (\fIx\fR), or set/fix (\fIs\fR) bad sites\&. The
+\fIw\fR
+option can be combined with
+\fIx\fR
+and
+\fIs\fR\&. Note that
+\fIs\fR
+can swap alleles and will update genotypes (GT) and AC counts, but will not attempt to fix PL or other fields\&.
+.RE
+.PP
+\fB\-d, \-\-rm\-dup\fR \fIsnps\fR|\fIindels\fR|\fIboth\fR|\fIall\fR|\fInone\fR
+.RS 4
+If a record is present in multiple files, output only the first instance, see
+\fB\-\-collapse\fR
+in
+\fBCommon Options\fR\&. Requires
+\fB\-a, \-\-allow\-overlaps\fR\&.
+.RE
 .PP
 \fB\-D, \-\-remove\-duplicates\fR
 .RS 4
-remove duplicate lines of the same type
+If a record is present in multiple files, output only the first instance\&. Alias for
+\fB\-d none\fR\&. Requires
+\fB\-a, \-\-allow\-overlaps\fR\&.
 .RE
 .PP
 \fB\-f, \-\-fasta\-ref\fR \fIFILE\fR
 .RS 4
-reference sequence
+reference sequence\&. Supplying this option will turn on left\-alignment and normalization, however, see also the
+\fB\-\-do\-not\-normalize\fR
+option below\&.
 .RE
 .PP
 \fB\-m, \-\-multiallelics\fR ←|+>[\fIsnps\fR|\fIindels\fR|\fIboth\fR|\fIany\fR]
@@ -1786,6 +2142,18 @@ split multiallelic sites into biallelic records (\fI\-\fR) or join biallelic sit
 \fIany\fR\&.
 .RE
 .PP
+\fB\-N, \-\-do\-not\-normalize\fR
+.RS 4
+the
+\fI\-c s\fR
+option can be used to fix or set the REF allele from the reference
+\fI\-f\fR\&. The
+\fI\-N\fR
+option will not turn on indel normalisation as the
+\fI\-f\fR
+option normally implies
+.RE
+.PP
 \fB\-o, \-\-output\fR \fIFILE\fR
 .RS 4
 see
@@ -1827,11 +2195,17 @@ see
 \fBCommon Options\fR
 .RE
 .PP
+\fB\-\-threads\fR \fIINT\fR
+.RS 4
+see
+\fBCommon Options\fR
+.RE
+.PP
 \fB\-w, \-\-site\-win\fR \fIINT\fR
 .RS 4
 maximum distance between two records to consider when locally sorting variants which changed position during the realignment
 .RE
-.SS "bcftools plugin \fINAME\fR \fI[OPTIONS]\fR \fIFILE\fR \(em \fI[PLUGIN OPTIONS]\fR"
+.SS "bcftools [plugin \fINAME\fR|+\fINAME\fR] \fI[OPTIONS]\fR \fIFILE\fR \(em \fI[PLUGIN OPTIONS]\fR"
 .sp
 .it 1 an-trap
 .nr an-no-space-flag 1
@@ -1901,6 +2275,12 @@ see
 see
 \fBCommon Options\fR
 .RE
+.PP
+\fB\-\-threads\fR \fIINT\fR
+.RS 4
+see
+\fBCommon Options\fR
+.RE
 .RE
 .sp
 .it 1 an-trap
@@ -1918,15 +2298,24 @@ list plugin\(cqs options
 .PP
 \fB\-l, \-\-list\-plugins\fR
 .RS 4
-List all available plugins\&. If not installed systemwide, set the environment variable LD_LIBRARY_PATH (linux) or DYLD_LIBRARY_PATH (Mac OS X) to include directory where
-\fBlibhts\&.so\fR
-is located\&. The BCFTOOLS_PLUGINS environment variable tells the program which directories to search\&.
+List all available plugins\&.
+.sp
+By default, appropriate system directories are searched for installed plugins\&. You can override this by setting the BCFTOOLS_PLUGINS environment variable to a colon\-separated list of directories to search\&. If BCFTOOLS_PLUGINS begins with a colon, ends with a colon, or contains adjacent colons, the system directories are also searched at that position in the list of directories\&.
+.sp
+If htslib is not installed systemwide, set the environment variable LD_LIBRARY_PATH (linux) or DYLD_LIBRARY_PATH (Mac OS X) to include the directory where
+\fBlibhts\&.so\&.1\fR
+is located\&.
 .RE
 .PP
 \fB\-v, \-\-verbose\fR
 .RS 4
 print debugging information to debug plugin failure
 .RE
+.PP
+\fB\-V, \-\-version\fR
+.RS 4
+print version string and exit
+.RE
 .RE
 .sp
 .it 1 an-trap
@@ -1996,9 +2385,13 @@ bcftools plugin
 # List available plugins
 bcftools plugin \-l
 
-# One can run plugins in several ways
+# Run a plugin
 bcftools plugin counts in\&.vcf
+
+# Run a plugin using the abbreviated "+" notation
 bcftools +counts in\&.vcf
+
+# The input VCF can be streamed just like in other commands
 cat in\&.vcf | bcftools +counts
 
 # Print usage information of plugin "dosage"
@@ -2134,6 +2527,101 @@ void destroy(void);
 .RE
 .\}
 .RE
+.SS "bcftools polysomy [\fIOPTIONS\fR] \fIfile\&.vcf\&.gz\fR"
+.sp
+Detect number of chromosomal copies in VCFs annotates with the Illumina\(cqs B\-allele frequency (BAF) values\&. Note that this command is not compiled in by default, see the section \fBOptional Compilation with GSL\fR in the INSTALL file for help\&.
+.sp
+.it 1 an-trap
+.nr an-no-space-flag 1
+.nr an-break-flag 1
+.br
+.ps +1
+\fBGeneral options:\fR
+.RS 4
+.PP
+\fB\-o, \-\-output\-dir\fR \fIpath\fR
+.RS 4
+output directory
+.RE
+.PP
+\fB\-r, \-\-regions\fR \fIchr\fR|\fIchr:pos\fR|\fIchr:from\-to\fR|\fIchr:from\-\fR[,\&...]
+.RS 4
+see
+\fBCommon Options\fR
+.RE
+.PP
+\fB\-R, \-\-regions\-file\fR \fIfile\fR
+.RS 4
+see
+\fBCommon Options\fR
+.RE
+.PP
+\fB\-s, \-\-sample\fR \fIstring\fR
+.RS 4
+samply name
+.RE
+.PP
+\fB\-t, \-\-targets\fR \fILIST\fR
+.RS 4
+see
+\fBCommon Options\fR
+.RE
+.PP
+\fB\-T, \-\-targets\-file\fR \fIFILE\fR
+.RS 4
+see
+\fBCommon Options\fR
+.RE
+.PP
+\fB\-v, \-\-verbose\fR
+.RS 4
+verbose debugging output which gives hints about the thresholds and decisions made by the program\&. Note that the exact output can change between versions\&.
+.RE
+.RE
+.sp
+.it 1 an-trap
+.nr an-no-space-flag 1
+.nr an-break-flag 1
+.br
+.ps +1
+\fBAlgorithm options:\fR
+.RS 4
+.PP
+\fB\-b, \-\-peak\-size\fR \fIfloat\fR
+.RS 4
+the minimum peak size considered as a good match can be from the interval [0,1] where larger is stricter
+.RE
+.PP
+\fB\-c, \-\-cn\-penalty\fR \fIfloat\fR
+.RS 4
+a penalty for increasing copy number state\&. How this works: multiple peaks are always a better fit than a single peak, therefore the program prefers a single peak (normal copy number) unless the absolute deviation of the multiple peaks fit is significantly smaller\&. Here the meaning of "significant" is given by the
+\fIfloat\fR
+from the interval [0,1] where larger is stricter\&.
+.RE
+.PP
+\fB\-f, \-\-fit\-th\fR \fIfloat\fR
+.RS 4
+threshold for goodness of fit (normalized absolute deviation), smaller is stricter
+.RE
+.PP
+\fB\-i, \-\-include\-aa\fR
+.RS 4
+include also the AA peak in CN2 and CN3 evaluation\&. This usually requires increasing
+\fB\-f\fR\&.
+.RE
+.PP
+\fB\-m, \-\-min\-fraction\fR \fIfloat\fR
+.RS 4
+minimum distinguishable fraction of aberrant cells\&. The experience shows that trustworthy are estimates of 20% and more\&.
+.RE
+.PP
+\fB\-p, \-\-peak\-symmetry\fR \fIfloat\fR
+.RS 4
+a heuristics to filter failed fits where the expected peak symmetry is violated\&. The
+\fIfloat\fR
+is from the interval [0,1] and larger is stricter
+.RE
+.RE
 .SS "bcftools query [\fIOPTIONS\fR] \fIfile\&.vcf\&.gz\fR [\fIfile\&.vcf\&.gz\fR [\&...]]"
 .sp
 Extracts fields from VCF or BCF files and outputs them in user\-defined format\&.
@@ -2217,6 +2705,11 @@ see
 \fBCommon Options\fR
 .RE
 .PP
+\fB\-u, \-\-allow\-undef\-tags\fR
+.RS 4
+do not throw an error if there are undefined tags in the format string, print "\&." instead
+.RE
+.PP
 \fB\-v, \-\-vcf\-list\fR \fIFILE\fR
 .RS 4
 process multiple VCFs listed in the file
@@ -2317,15 +2810,13 @@ Emission probabilities:
 Transition probabilities:
   tAZ = P(AZ|HW)  \&.\&. from HW to AZ, the \-a parameter
   tHW = P(HW|AZ)  \&.\&. from AZ to HW, the \-H parameter
-  P(AZ|AZ) = 1 \- P(HW|AZ) = 1 \- tHW
-  P(HW|HW) = 1 \- P(AZ|HW) = 1 \- tAZ
 
   ci  = P_i(C)  \&.\&. probability of cross\-over at site i, from genetic map
   AZi = P_i(AZ) \&.\&. probability of site i being AZ/non\-AZ, scaled so that AZi+HWi = 1
   HWi = P_i(HW)
 
-  P_{i+1}(AZ) = oAZ * max[(1\-tHW) * (1\-ci) * AZ{i\-1} , tAZ * ci * (1\-AZ{i\-1})]
-  P_{i+1}(HW) = oHW * max[(1\-tAZ) * (1\-ci) * (1\-AZ{i\-1}) , tHW * ci * AZ{i\-1}]
+  P_{i+1}(AZ) = oAZ * max[(1 \- tAZ * ci) * AZ{i\-1} , tAZ * ci * (1\-AZ{i\-1})]
+  P_{i+1}(HW) = oHW * max[(1 \- tHW * ci) * (1\-AZ{i\-1}) , tHW * ci * AZ{i\-1}]
 .fi
 .if n \{\
 .RE
@@ -2340,6 +2831,12 @@ Transition probabilities:
 \fBGeneral Options:\fR
 .RS 4
 .PP
+\fB\-\-AF\-dflt\fR \fIFLOAT\fR
+.RS 4
+in case allele frequency is not known, use the
+\fIFLOAT\fR\&. By default, sites where allele frequency cannot be determined, or is 0, are skipped\&.
+.RE
+.PP
 \fB\-\-AF\-tag\fR \fITAG\fR
 .RS 4
 use the specified INFO tag
@@ -2392,6 +2889,11 @@ genetic map in the format required also by IMPUTE2\&. Only the first and third c
 can chromosome name\&.
 .RE
 .PP
+\fB\-M, \-\-rec\-rate\fR \fIFLOAT\fR
+.RS 4
+constant recombination rate per bp
+.RE
+.PP
 \fB\-r, \-\-regions\fR \fIchr\fR|\fIchr:pos\fR|\fIchr:from\-to\fR|\fIchr:from\-\fR[,\&...]
 .RS 4
 see
@@ -2451,7 +2953,7 @@ Parses VCF or BCF and produces text file stats which is suitable for machine pro
 .PP
 \fB\-1, \-\-1st\-allele\-only\fR
 .RS 4
-consider only 1st allele at multiallelic sites
+consider only the 1st alternate allele at multiallelic sites
 .RE
 .PP
 \fB\-c, \-\-collapse\fR \fIsnps\fR|\fIindels\fR|\fIboth\fR|\fIall\fR|\fIsome\fR|\fInone\fR
@@ -2470,7 +2972,15 @@ ranges of depth distribution: min, max, and size of the bin
 produce verbose per\-site and per\-sample output
 .RE
 .PP
-\fB\-e, \-\-exons\fR \fIfile\&.gz\fR
+\fB\-e, \-\-exclude\fR \fIEXPRESSION\fR
+.RS 4
+exclude sites for which
+\fIEXPRESSION\fR
+is true\&. For valid expressions see
+\fBEXPRESSIONS\fR\&.
+.RE
+.PP
+\fB\-E, \-\-exons\fR \fIfile\&.gz\fR
 .RS 4
 tab\-delimited file with exons for indel frameshifts statistics\&. The columns of the file are CHR, FROM, TO, with 1\-based, inclusive, positions\&. The file is BGZF\-compressed and indexed with tabix
 .RE
@@ -2496,7 +3006,15 @@ see
 faidx indexed reference sequence file to determine INDEL context
 .RE
 .PP
-\fB\-i, \-\-split\-by\-ID\fR
+\fB\-i, \-\-include\fR \fIEXPRESSION\fR
+.RS 4
+include only sites for which
+\fIEXPRESSION\fR
+is true\&. For valid expressions see
+\fBEXPRESSIONS\fR\&.
+.RE
+.PP
+\fB\-I, \-\-split\-by\-ID\fR
 .RS 4
 collect stats separately for sites which have the ID column set ("known sites") or which do not have the ID column set ("novel sites")\&.
 .RE
@@ -2536,6 +3054,16 @@ see
 see
 \fBCommon Options\fR
 .RE
+.PP
+\fB\-u, \-\-user\-tstv\fR \fI<TAG[:min:max:n]>\fR
+.RS 4
+collect Ts/Tv stats for any tag using the given binning [0:1:100]
+.RE
+.PP
+\fB\-v, \-\-verbose\fR
+.RS 4
+produce verbose per\-site and per\-sample output
+.RE
 .SS "bcftools view [\fIOPTIONS\fR] \fIfile\&.vcf\&.gz\fR [\fIREGION\fR [\&...]]"
 .sp
 View, subset and filter VCF or BCF files by position and filtering expression\&. Convert between VCF and BCF\&. Former \fBbcftools subset\fR\&.
@@ -2601,6 +3129,12 @@ see
 see
 \fBCommon Options\fR
 .RE
+.PP
+\fB\-\-threads\fR \fIINT\fR
+.RS 4
+see
+\fBCommon Options\fR
+.RE
 .RE
 .sp
 .it 1 an-trap
@@ -2616,6 +3150,11 @@ see
 trim alternate alleles not seen in subset\&. Type A, G and R INFO and FORMAT fields will also be trimmed
 .RE
 .PP
+\fB\-\-force\-samples\fR
+.RS 4
+only warn about unknown subset samples
+.RE
+.PP
 \fB\-I, \-\-no\-update\fR
 .RS 4
 do not (re)calculate INFO fields for the subset (currently INFO/AC and INFO/AN)
@@ -2718,12 +3257,12 @@ print sites where all samples are phased\&. Haploid genotypes are considered pha
 exclude sites where all samples are phased
 .RE
 .PP
-\fB\-q, \-\-min\-af\fR \fIFLOAT\fR[\fI:nref\fR|\fI:alt1\fR|\fI:minor\fR|:\*(Aqmajor\*(Aq|:\*(Aqnonmajor\*(Aq]
+\fB\-q, \-\-min\-af\fR \fIFLOAT\fR[\fI:nref\fR|\fI:alt1\fR|\fI:minor\fR|\fI:major\fR|\fI:nonmajor\fR]
 .RS 4
 minimum allele frequency (INFO/AC / INFO/AN) of sites to be printed\&. Specifying the type of allele is optional and can be set to non\-reference (\fInref\fR, the default), 1st alternate (\fIalt1\fR), the least frequent (\fIminor\fR), the most frequent (\fImajor\fR) or sum of all but the most frequent (\fInonmajor\fR) alleles\&.
 .RE
 .PP
-\fB\-Q, \-\-max\-af\fR \fIFLOAT\fR[\fI:nref\fR|\fI:alt1\fR|\fI:minor\fR|:\*(Aqmajor\*(Aq|:\*(Aqnonmajor\*(Aq]
+\fB\-Q, \-\-max\-af\fR \fIFLOAT\fR[\fI:nref\fR|\fI:alt1\fR|\fI:minor\fR|\fI:major\fR|\fI:nonmajor\fR]
 .RS 4
 maximum allele frequency (INFO/AC / INFO/AN) of sites to be printed\&. Specifying the type of allele is optional and can be set to non\-reference (\fInref\fR, the default), 1st alternate (\fIalt1\fR), the least frequent (\fIminor\fR), the most frequent (\fImajor\fR) or sum of all but the most frequent (\fInonmajor\fR) alleles\&.
 .RE
@@ -2740,17 +3279,24 @@ exclude sites without a called genotype
 .PP
 \fB\-v, \-\-types\fR \fIsnps\fR|\fIindels\fR|\fImnps\fR|\fIother\fR
 .RS 4
-comma\-separated list of variant types to select
+comma\-separated list of variant types to select\&. Site is selected if any of the ALT alleles is of the type requested\&. Types are determined by comparing the REF and ALT alleles in the VCF record not INFO tags like INFO/INDEL or INFO/VT\&. Use
+\fB\-\-include\fR
+to select based on INFO tags\&.
 .RE
 .PP
 \fB\-V, \-\-exclude\-types\fR \fIsnps\fR|\fIindels\fR|\fImnps\fR|\fIother\fR
 .RS 4
-comma\-separated list of variant types to exclude
+comma\-separated list of variant types to exclude\&. Site is excluded if any of the ALT alleles is of the type requested\&. Types are determined by comparing the REF and ALT alleles in the VCF record not INFO tags like INFO/INDEL or INFO/VT\&. Use
+\fB\-\-exclude\fR
+to exclude based on INFO tags\&.
 .RE
 .PP
 \fB\-x, \-\-private\fR
 .RS 4
-print sites where only the subset samples carry an non\-reference allele
+print sites where only the subset samples carry an non\-reference allele\&. Requires
+\fB\-\-samples\fR
+or
+\fB\-\-samples\-file\fR\&.
 .RE
 .PP
 \fB\-X, \-\-exclude\-private\fR
@@ -2758,6 +3304,15 @@ print sites where only the subset samples carry an non\-reference allele
 exclude sites where only the subset samples carry an non\-reference allele
 .RE
 .RE
+.SS "bcftools help [\fICOMMAND\fR] | bcftools \-\-help [\fICOMMAND\fR]"
+.sp
+Display a brief usage message listing the bcftools commands available\&. If the name of a command is also given, e\&.g\&., bcftools help view, the detailed usage message for that particular command is displayed\&.
+.SS "bcftools [\fI\-\-version\fR|\fI\-v\fR]"
+.sp
+Display the version numbers and copyright information for bcftools and the important libraries used by bcftools\&.
+.SS "bcftools [\fI\-\-version\-only\fR]"
+.sp
+Display the full bcftools version number in a machine\-readable format\&.
 .SH "EXPRESSIONS"
 .sp
 These filtering expressions are accepted by \fBannotate\fR, \fBfilter\fR, \fBquery\fR and \fBview\fR commands\&.
@@ -2908,7 +3463,7 @@ INFO tags, FORMAT tags, column names
 .nf
 INFO/DP or DP
 FORMAT/DV, FMT/DV, or DV
-FILTER, QUAL, ID, REF, ALT[0]
+FILTER, QUAL, ID, POS, REF, ALT[0]
 .fi
 .if n \{\
 .RE
@@ -2944,6 +3499,48 @@ FlagA=1 && FlagB=0
 .sp -1
 .IP \(bu 2.3
 .\}
+"\&." to test missing values
+.sp
+.if n \{\
+.RS 4
+.\}
+.nf
+DP="\&.", DP!="\&.", ALT="\&."
+.fi
+.if n \{\
+.RE
+.\}
+.RE
+.sp
+.RS 4
+.ie n \{\
+\h'-04'\(bu\h'+03'\c
+.\}
+.el \{\
+.sp -1
+.IP \(bu 2.3
+.\}
+missing genotypes can be matched regardless of phase and ploidy ("\&.|\&.", "\&./\&.", "\&.") using this expression
+.sp
+.if n \{\
+.RS 4
+.\}
+.nf
+GT="\&."
+.fi
+.if n \{\
+.RE
+.\}
+.RE
+.sp
+.RS 4
+.ie n \{\
+\h'-04'\(bu\h'+03'\c
+.\}
+.el \{\
+.sp -1
+.IP \(bu 2.3
+.\}
 TYPE for variant type in REF,ALT columns (indel,snp,mnp,ref,other)
 .sp
 .if n \{\
@@ -3093,6 +3690,26 @@ MIN(DP)>10 & MIN(DV)>3
 .RS 4
 .\}
 .nf
+FMT/DP>10  & FMT/GQ>10 \&.\&. both conditions must be satisfied within one sample
+.fi
+.if n \{\
+.RE
+.\}
+.sp
+.if n \{\
+.RS 4
+.\}
+.nf
+FMT/DP>10 && FMT/GQ>10 \&.\&. the conditions can be satisfied in different samples
+.fi
+.if n \{\
+.RE
+.\}
+.sp
+.if n \{\
+.RS 4
+.\}
+.nf
 QUAL>10 |  FMT/GQ>10   \&.\&. selects only GQ>10 samples
 .fi
 .if n \{\
@@ -3159,6 +3776,16 @@ MAF[0]<0\&.05    \&.\&. select rare variants at 5% cutoff
 .RE
 .\}
 .sp
+.if n \{\
+.RS 4
+.\}
+.nf
+POS>=100   \&.\&. restrict your range query, e\&.g\&. 20:100\-200 to strictly sites with POS in that range\&.
+.fi
+.if n \{\
+.RE
+.\}
+.sp
 \fBShell expansion:\fR
 .sp
 Note that expressions must often be quoted because some characters have special meaning in the shell\&. An example of expression enclosed in single quotes which cause that the whole expression is passed to the program as intended:
diff --git a/doc/bcftools.html b/doc/bcftools.html
index ef1b841..012d670 100644
--- a/doc/bcftools.html
+++ b/doc/bcftools.html
@@ -1,13 +1,14 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8" /><title>bcftools</title><link rel="stylesheet" type="text/css" href="docbook-xsl.css" /><meta name="generator" content="DocBook XSL Stylesheets V1.76.1" /></head><body><div xml:lang="en" class="refentry" title="bcftools" lang="en"><a id="idp25137184"></a><div class="titlepage"></div><div class="refnamediv"><h2>Name</h2><p>bcftools — utilities for variant calling and manipu [...]
+<html xmlns="http://www.w3.org/1999/xhtml"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8" /><title>bcftools</title><link rel="stylesheet" type="text/css" href="docbook-xsl.css" /><meta name="generator" content="DocBook XSL Stylesheets V1.76.1" /></head><body><div xml:lang="en" class="refentry" title="bcftools" lang="en"><a id="idp1931920"></a><div class="titlepage"></div><div class="refnamediv"><h2>Name</h2><p>bcftools — utilities for variant calling and manipul [...]
 Call Format (VCF) and its binary counterpart BCF. All commands work
 transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.</p><p>Most commands accept VCF, bgzipped VCF and BCF with filetype detected
 automatically even when streaming from a pipe. Indexed VCF and BCF
 will work in all situations. Un-indexed VCF and BCF and streams will
-work in most, but not all situations.</p><p>BCFtools is designed to work on a stream. It regards an input file "-" as the
+work in most, but not all situations. In general, whenever multiple VCFs are
+read simultaneously, they must be indexed and therefore also compressed.</p><p>BCFtools is designed to work on a stream. It regards an input file "-" as the
 standard input (stdin) and outputs to the standard output (stdout). Several
-commands can thus be  combined  with  Unix pipes.</p><div class="refsect2" title="VERSION"><a id="_version"></a><h3>VERSION</h3><p>This manual page was last updated <span class="strong"><strong>2015-01-21 15:01 GMT</strong></span> and refers to bcftools git version <span class="strong"><strong>1.1-140-g9b0e7cc+</strong></span>.</p></div><div class="refsect2" title="BCF1"><a id="_bcf1"></a><h3>BCF1</h3><p>The BCF1 format output by versions of samtools <= 0.1.19 is <span class="strong"> [...]
+commands can thus be  combined  with  Unix pipes.</p><div class="refsect2" title="VERSION"><a id="_version"></a><h3>VERSION</h3><p>This manual page was last updated <span class="strong"><strong>2015-12-15 14:02 GMT</strong></span> and refers to bcftools git version <span class="strong"><strong>1.2-191-g6737c5c+</strong></span>.</p></div><div class="refsect2" title="BCF1"><a id="_bcf1"></a><h3>BCF1</h3><p>The BCF1 format output by versions of samtools <= 0.1.19 is <span class="strong"> [...]
 compatible with this version of bcftools. To read BCF1 files one can use
 the view command from old versions of bcftools packaged with samtools
 versions <= 0.1.19 to convert to VCF, which can then be read by
@@ -22,6 +23,8 @@ list of available options, run <span class="strong"><strong>bcftools</strong></s
 </li><li class="listitem">
 <span class="strong"><strong><a class="link" href="#call" title="bcftools call [OPTIONS] FILE">call</a></strong></span>        ..  SNP/indel calling (former "view")
 </li><li class="listitem">
+<span class="strong"><strong><a class="link" href="#cnv" title="bcftools cnv [OPTIONS] FILE">cnv</a></strong></span>          ..  Copy Number Variation caller
+</li><li class="listitem">
 <span class="strong"><strong><a class="link" href="#concat" title="bcftools concat [OPTIONS] FILE1 FILE2 […]">concat</a></strong></span>    ..  concatenate VCF/BCF files from the same set of samples
 </li><li class="listitem">
 <span class="strong"><strong><a class="link" href="#consensus" title="bcftools consensus [OPTIONS] FILE">consensus</a></strong></span>    ..  create consensus sequence by applying VCF variants
@@ -40,7 +43,9 @@ list of available options, run <span class="strong"><strong>bcftools</strong></s
 </li><li class="listitem">
 <span class="strong"><strong><a class="link" href="#norm" title="bcftools norm [OPTIONS] file.vcf.gz">norm</a></strong></span>        ..  normalize indels
 </li><li class="listitem">
-<span class="strong"><strong><a class="link" href="#plugin" title="bcftools plugin NAME [OPTIONS] FILE — [PLUGIN OPTIONS]">plugin</a></strong></span>    ..  run user-defined plugin
+<span class="strong"><strong><a class="link" href="#plugin" title="bcftools [plugin NAME|+NAME] [OPTIONS] FILE — [PLUGIN OPTIONS]">plugin</a></strong></span>    ..  run user-defined plugin
+</li><li class="listitem">
+<span class="strong"><strong><a class="link" href="#polysomy" title="bcftools polysomy [OPTIONS] file.vcf.gz">polysomy</a></strong></span>   ..  detect contaminations and whole-chromosome aberrations
 </li><li class="listitem">
 <span class="strong"><strong><a class="link" href="#query" title="bcftools query [OPTIONS] file.vcf.gz [file.vcf.gz […]]">query</a></strong></span>      ..  transform VCF/BCF into user-defined formats
 </li><li class="listitem">
@@ -120,6 +125,9 @@ specific commands to see if they apply.</p><div class="variablelist"><dl><dt><sp
 <span class="strong"><strong>-O, --output-type</strong></span> <span class="emphasis"><em>b</em></span>|<span class="emphasis"><em>u</em></span>|<span class="emphasis"><em>z</em></span>|<span class="emphasis"><em>v</em></span>
 </span></dt><dd>
     Output compressed BCF (<span class="emphasis"><em>b</em></span>), uncompressed BCF (<span class="emphasis"><em>u</em></span>), compressed VCF (<span class="emphasis"><em>z</em></span>), uncompressed VCF (<span class="emphasis"><em>v</em></span>).
+    Use the -Ou option when piping between bcftools subcommands to speed up
+    performance by removing unecessary compression/decompression and
+    VCF←→BCF conversion.
 </dd><dt><span class="term">
 <span class="strong"><strong>-r, --regions</strong></span> <span class="emphasis"><em>chr</em></span>|<span class="emphasis"><em>chr:pos</em></span>|<span class="emphasis"><em>chr:from-to</em></span>|<span class="emphasis"><em>chr:from-</em></span>[,…]
 </span></dt><dd>
@@ -147,15 +155,40 @@ specific commands to see if they apply.</p><div class="variablelist"><dl><dt><sp
 </span></dt><dd>
     Comma-separated list of samples to include or exclude if prefixed
     with "^".
-</dd><dt><span class="term">
-<span class="strong"><strong>-S, --samples-file</strong></span> <span class="emphasis"><em><span class="^">FILE</span></em></span>
+    Note that in general tags such as INFO/AC, INFO/AN, etc are not updated
+    to correspond to the subset samples. <span class="strong"><strong><a class="link" href="#view" title="bcftools view [OPTIONS] file.vcf.gz [REGION […]]">bcftools view</a></strong></span> is the
+    exception where some tags will be updated (unless the <span class="strong"><strong>-I, --no-update</strong></span>
+    option is used; see <span class="strong"><strong><a class="link" href="#view" title="bcftools view [OPTIONS] file.vcf.gz [REGION […]]">bcftools view</a></strong></span> documentation). To use updated
+    tags for the subset in another command one can pipe from <span class="strong"><strong>view</strong></span> into
+    that command. For example:
+</dd></dl></div><pre class="screen">    bcftools view -Ou -s sample1,sample2 file.vcf | bcftools query -f %INFO/AC\t%INFO/AN\n</pre><div class="variablelist"><dl><dt><span class="term">
+<span class="strong"><strong>-S, --samples-file</strong></span> <span class="emphasis"><em><span class="^">FILE</span></em></span><a id="samples_file"></a>
 </span></dt><dd>
     File of sample names to include or exclude if prefixed with "^".
-    One sample per line.
+    One sample per line. See also the note above for the <span class="strong"><strong>-s, --samples</strong></span>
+    option.
     The command <span class="strong"><strong><a class="link" href="#call" title="bcftools call [OPTIONS] FILE">bcftools call</a></strong></span> accepts an optional second
-    column indicating ploidy (0, 1 or 2) and can parse also PED files.
-    With <span class="strong"><strong><a class="link" href="#call" title="bcftools call [OPTIONS] FILE">bcftools call</a> -C</strong></span> <span class="emphasis"><em>trio</em></span>, PED file is expected.
-</dd><dt><span class="term">
+    column indicating ploidy (0, 1 or 2) or sex (as defined by
+    <span class="strong"><strong><a class="link" href="#ploidy">--ploidy</a></strong></span>, for example "F" or "M"), and can parse also PED
+    files. If the second column is not present,
+    the sex "F" is assumed.
+    With <span class="strong"><strong><a class="link" href="#call" title="bcftools call [OPTIONS] FILE">bcftools call</a> -C</strong></span> <span class="emphasis"><em>trio</em></span>, PED file is expected. File
+    formats examples:
+</dd></dl></div><pre class="screen">    sample1    1
+    sample2    2
+    sample3    2
+
+  or
+
+    sample1    M
+    sample2    F
+    sample3    F
+
+  or a .ped file (here is shown a minimum working example, the first column is
+  ignored and the last indicates sex: 1=male, 2=female)
+
+    ignored daughterA fatherA motherA 2
+    ignored sonB fatherB motherB 1</pre><div class="variablelist"><dl><dt><span class="term">
 <span class="strong"><strong>-t, --targets</strong></span> [^]<span class="emphasis"><em>chr</em></span>|<span class="emphasis"><em>chr:pos</em></span>|<span class="emphasis"><em>chr:from-to</em></span>|<span class="emphasis"><em>chr:from-</em></span>[,…]
 </span></dt><dd>
     Similar as <span class="strong"><strong>-r, --regions</strong></span>, but the next position is accessed by streaming the
@@ -177,8 +210,14 @@ specific commands to see if they apply.</p><div class="variablelist"><dl><dt><sp
 </span></dt><dd>
     With the <span class="strong"><strong>call -C</strong></span> <span class="emphasis"><em>alleles</em></span> command, third column of the targets file must
     be comma-separated list of alleles, starting with the reference allele.
+    Note that the file must be compressed and index.
     Such a file can be easily created from a VCF using:
-</dd></dl></div><pre class="screen">    bcftools query -f'%CHROM\t%POS\t%REF,%ALT\n' file.vcf</pre></div><div class="refsect2" title="bcftools annotate [OPTIONS] FILE"><a id="annotate"></a><h3>bcftools annotate <span class="emphasis"><em>[OPTIONS]</em></span> <span class="emphasis"><em>FILE</em></span></h3><p>This command allows to add or remove annotations.</p><div class="variablelist"><dl><dt><span class="term">
+</dd></dl></div><pre class="screen">    bcftools query -f'%CHROM\t%POS\t%REF,%ALT\n' file.vcf | bgzip -c > als.tsv.gz && tabix -s1 -b2 -e2 als.tsv.gz</pre><div class="variablelist"><dl><dt><span class="term">
+<span class="strong"><strong>--threads</strong></span> <span class="emphasis"><em>INT</em></span>
+</span></dt><dd>
+    Number of output compression threads to use in addition to main thread.
+    Only used when <span class="emphasis"><em>--output-type</em></span> is <span class="emphasis"><em>b</em></span> or <span class="emphasis"><em>z</em></span>. Default: 0.
+</dd></dl></div></div><div class="refsect2" title="bcftools annotate [OPTIONS] FILE"><a id="annotate"></a><h3>bcftools annotate <span class="emphasis"><em>[OPTIONS]</em></span> <span class="emphasis"><em>FILE</em></span></h3><p>This command allows to add or remove annotations.</p><div class="variablelist"><dl><dt><span class="term">
 <span class="strong"><strong>-a, --annotations</strong></span> <span class="emphasis"><em>file</em></span>
 </span></dt><dd>
     Bgzip-compressed and tabix-indexed file with annotations. The file
@@ -214,8 +253,11 @@ specific commands to see if they apply.</p><div class="variablelist"><dl><dt><sp
     can be edited, where INFO tags can be written both as "INFO/TAG" or simply "TAG",
     and FORMAT tags can be written as "FORMAT/TAG" or "FMT/TAG".
     To carry over all INFO annotations, use "INFO". To add all INFO annotations except
-    "TAG", use "^INFO/TAG". By default, existing values are replaced. To add
-    values without overwriting existing annotations, use "+TAG" instead of "TAG".
+    "TAG", use "^INFO/TAG". By default, existing values are replaced.
+    To add annotations without overwriting existing values (that is, to add missing tags or
+    add values to existing tags with missing values), use "+TAG" instead of "TAG".
+    To append to existing values (rather than replacing or leaving untouched), use "=TAG"
+    (instead of "TAG" or "+TAG").
     To replace only existing values without modifying missing annotations, use "-TAG".
     If the annotation file is not a VCF/BCF, all new annotations must be
     defined via <span class="strong"><strong>-h, --header-lines</strong></span>.
@@ -242,6 +284,10 @@ specific commands to see if they apply.</p><div class="variablelist"><dl><dt><sp
     include only sites for which <span class="emphasis"><em>EXPRESSION</em></span> is true. For valid expressions see
     <span class="strong"><strong><a class="link" href="#expressions" title="EXPRESSIONS">EXPRESSIONS</a></strong></span>.
 </dd><dt><span class="term">
+<span class="strong"><strong>-m, --mark-sites</strong></span> <span class="emphasis"><em><span class="+-">TAG</span></em></span>
+</span></dt><dd>
+    annotate sites which are present ("+") or absent ("-") in the <span class="strong"><strong>-a</strong></span> file with a new INFO/TAG flag
+</dd><dt><span class="term">
 <span class="strong"><strong>-o, --output</strong></span> <span class="emphasis"><em>FILE</em></span>
 </span></dt><dd>
     see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
@@ -275,6 +321,10 @@ specific commands to see if they apply.</p><div class="variablelist"><dl><dt><sp
     given as "src_name dst_name\n", separated by whitespaces, each pair on a
     separate line.
 </dd><dt><span class="term">
+<span class="strong"><strong>--threads</strong></span> <span class="emphasis"><em>INT</em></span>
+</span></dt><dd>
+    see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
+</dd><dt><span class="term">
 <span class="strong"><strong>-x, --remove</strong></span> <span class="emphasis"><em>list</em></span>
 </span></dt><dd>
     List of annotations to remove. Use "FILTER" to remove all filters or
@@ -305,14 +355,130 @@ specific commands to see if they apply.</p><div class="variablelist"><dl><dt><sp
     bcftools annotate -a annots.tab.gz -h annots.hdr -c CHROM,FROM,TO,TAG inut.vcf
 
     # Annotate from a bed file (0-based coordinates, half-closed, half-open intervals)
-    bcftools annotate -a annots.bed.gz -h annots.hdr -c CHROM,FROM,TO,TAG input.vcf</pre></div><div class="refsect2" title="bcftools call [OPTIONS] FILE"><a id="call"></a><h3>bcftools call <span class="emphasis"><em>[OPTIONS]</em></span> <span class="emphasis"><em>FILE</em></span></h3><p>This command replaces the former <span class="strong"><strong>bcftools view</strong></span> caller. Some of the original
+    bcftools annotate -a annots.bed.gz -h annots.hdr -c CHROM,FROM,TO,TAG input.vcf</pre></div><div class="refsect2" title="bcftools cnv [OPTIONS] FILE"><a id="cnv"></a><h3>bcftools cnv <span class="emphasis"><em>[OPTIONS]</em></span> <span class="emphasis"><em>FILE</em></span></h3><p>Copy number variation caller, requires a VCF annotated with the Illumina’s
+B-allele frequency (BAF) and Log R Ratio intensity (LRR) values. The HMM
+considers the following copy number states: CN 2 (normal), 1 (single-copy
+loss), 0 (complete loss), 3 (single-copy gain).</p><div class="refsect3" title="General Options:"><a id="_general_options"></a><h4>General Options:</h4><div class="variablelist"><dl><dt><span class="term">
+<span class="strong"><strong>-c, --control-sample</strong></span> <span class="emphasis"><em>string</em></span>
+</span></dt><dd>
+    optional control sample name. If given, pairwise calling is performed
+    and the <span class="strong"><strong>-P</strong></span>  option can be used
+</dd><dt><span class="term">
+<span class="strong"><strong>-f, --AF-file</strong></span> <span class="emphasis"><em>file</em></span>
+</span></dt><dd>
+    read allele frequencies from  a tab-delimited file with the columns CHR,POS,REF,ALT,AF
+</dd><dt><span class="term">
+*-o, --output-dir <span class="emphasis"><em>path</em></span>
+</span></dt><dd>
+    output directory
+</dd><dt><span class="term">
+*-p, --plot-threshold <span class="emphasis"><em>float</em></span>
+</span></dt><dd>
+    call <span class="strong"><strong>matplotlib</strong></span> to produce plots for chromosomes with quality at least <span class="emphasis"><em>float</em></span>,
+    useful for visual inspection of the calls. With <span class="strong"><strong>-p 0</strong></span>, plots for all chromosomes will be
+    generated. If not given, a <span class="strong"><strong>matplotlib</strong></span> script will be created but not called.
+</dd><dt><span class="term">
+<span class="strong"><strong>-r, --regions</strong></span> <span class="emphasis"><em>chr</em></span>|<span class="emphasis"><em>chr:pos</em></span>|<span class="emphasis"><em>chr:from-to</em></span>|<span class="emphasis"><em>chr:from-</em></span>[,…]
+</span></dt><dd>
+    see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
+</dd><dt><span class="term">
+<span class="strong"><strong>-R, --regions-file</strong></span> <span class="emphasis"><em>file</em></span>
+</span></dt><dd>
+    see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
+</dd><dt><span class="term">
+<span class="strong"><strong>-s, --query-sample</strong></span> <span class="emphasis"><em>string</em></span>
+</span></dt><dd>
+    query samply name
+</dd><dt><span class="term">
+<span class="strong"><strong>-t, --targets</strong></span> <span class="emphasis"><em>LIST</em></span>
+</span></dt><dd>
+    see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
+</dd><dt><span class="term">
+<span class="strong"><strong>-T, --targets-file</strong></span> <span class="emphasis"><em>FILE</em></span>
+</span></dt><dd>
+    see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
+</dd></dl></div></div><div class="refsect3" title="HMM Options:"><a id="_hmm_options"></a><h4>HMM Options:</h4><div class="variablelist"><dl><dt><span class="term">
+<span class="strong"><strong>-a, --aberrant</strong></span> <span class="emphasis"><em>float</em></span>[,<span class="emphasis"><em>float</em></span>]
+</span></dt><dd>
+    fraction of aberrant cells in query and control. The hallmark of
+    duplications and contaminations is the BAF value of heterozygous markers
+    which is dependent on the fraction of aberrant cells. Sensitivity to
+    smaller fractions of cells can be increased by setting <span class="strong"><strong>-a</strong></span> to a lower value. Note
+    however, that this comes at the cost of increased false discovery rate.
+</dd><dt><span class="term">
+<span class="strong"><strong>-b, --BAF-weight</strong></span> <span class="emphasis"><em>float</em></span>
+</span></dt><dd>
+    relative contribution from BAF
+</dd><dt><span class="term">
+<span class="strong"><strong>d, --BAF-dev</strong></span> <span class="emphasis"><em>float</em></span>[,<span class="emphasis"><em>float</em></span>]
+</span></dt><dd>
+    expected BAF deviation in query and control, i.e. the noise observed
+    in the data.
+</dd><dt><span class="term">
+<span class="strong"><strong>-e, --err-prob</strong></span> <span class="emphasis"><em>float</em></span>
+</span></dt><dd>
+    uniform error probability
+</dd><dt><span class="term">
+<span class="strong"><strong>-l, --LRR-weight</strong></span> <span class="emphasis"><em>float</em></span>
+</span></dt><dd>
+    relative contribution from LRR. With noisy data, this option can have big effect
+    on the number of calls produced. In truly random noise (such as in simulated data),
+    the value should be set high (1.0), but in the presence of systematic noise
+    when LRR are not informative, lower values result in cleaner calls (0.2).
+</dd><dt><span class="term">
+<span class="strong"><strong>-L, --LRR-smooth-win</strong></span> <span class="emphasis"><em>int</em></span>
+</span></dt><dd>
+    reduce LRR noise by applying moving average given this window size
+</dd><dt><span class="term">
+<span class="strong"><strong>-O, --optimize</strong></span> <span class="emphasis"><em>float</em></span>
+</span></dt><dd>
+    iteratively estimate the fraction of aberrant cells, down to the given fraction.
+    Lowering this value from the default 1.0 to say, 0.3, can help discover more
+    events but also increases noise
+</dd><dt><span class="term">
+<span class="strong"><strong>-P, --same-prob</strong></span> <span class="emphasis"><em>float</em></span>
+</span></dt><dd>
+    the prior probability of the query and the control sample being the same.
+    Setting to 0 calls both independently, setting to 1 forces the same copy
+    number state in both.
+</dd><dt><span class="term">
+<span class="strong"><strong>-x, --xy-prob</strong></span> <span class="emphasis"><em>float</em></span>
+</span></dt><dd>
+    the HMM probability of transition to another copy number state. Increasing this
+    values leads to smaller and more frequent calls.
+</dd></dl></div></div></div><div class="refsect2" title="bcftools call [OPTIONS] FILE"><a id="call"></a><h3>bcftools call <span class="emphasis"><em>[OPTIONS]</em></span> <span class="emphasis"><em>FILE</em></span></h3><p>This command replaces the former <span class="strong"><strong>bcftools view</strong></span> caller. Some of the original
 functionality has been temporarily lost in the process of transition under
 <a class="ulink" href="http://github.com/samtools/htslib" target="_top">htslib</a>, but will be added back on popular
 demand. The original calling model can be invoked with the <span class="strong"><strong>-c</strong></span> option.</p><div class="refsect3" title="File format options:"><a id="_file_format_options"></a><h4>File format options:</h4><div class="variablelist"><dl><dt><span class="term">
+<span class="strong"><strong>-o, --output</strong></span> <span class="emphasis"><em>FILE</em></span>
+</span></dt><dd>
+    see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
+</dd><dt><span class="term">
 <span class="strong"><strong>-O, --output-type</strong></span> <span class="emphasis"><em>b</em></span>|<span class="emphasis"><em>u</em></span>|<span class="emphasis"><em>z</em></span>|<span class="emphasis"><em>v</em></span>
 </span></dt><dd>
     see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
 </dd><dt><span class="term">
+<span class="strong"><strong>--ploidy</strong></span> <span class="emphasis"><em>ASSEMBLY</em></span>[<span class="emphasis"><em>?</em></span>]<a id="ploidy"></a>
+</span></dt><dd>
+    predefined ploidy, use <span class="emphasis"><em>list</em></span> (or any other unused word) to print a list
+    of all predefined assemblies. Append a question mark to print the actual
+    definition. See also <span class="strong"><strong>--ploidy-file</strong></span>.
+</dd><dt><span class="term">
+<span class="strong"><strong>--ploidy-file</strong></span> <span class="emphasis"><em>FILE</em></span>
+</span></dt><dd>
+    ploidy definition given as a space/tab-delimited list of
+    CHROM, FROM, TO, SEX, PLOIDY. The SEX codes are arbitrary and
+    correspond to the ones used by <span class="strong"><strong><a class="link" href="#samples_file">--samples-file</a></strong></span>.
+    The default ploidy can be given using the starred records (see
+    below), unlisted regions have ploidy 2. The default ploidy definition is
+</dd></dl></div><pre class="screen">    X 1 60000 M 1
+    X 2699521 154931043 M 1
+    Y 1 59373566 M 1
+    Y 1 59373566 F 0
+    MT 1 16569 M 1
+    MT 1 16569 F 1
+    *  * *     M 2
+    *  * *     F 2</pre><div class="variablelist"><dl><dt><span class="term">
 <span class="strong"><strong>-r, --regions</strong></span> <span class="emphasis"><em>chr</em></span>|<span class="emphasis"><em>chr:pos</em></span>|<span class="emphasis"><em>chr:from-to</em></span>|<span class="emphasis"><em>chr:from-</em></span>[,…]
 </span></dt><dd>
     see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
@@ -336,6 +502,10 @@ demand. The original calling model can be invoked with the <span class="strong">
 <span class="strong"><strong>-T, --targets-file</strong></span> <span class="emphasis"><em>FILE</em></span>
 </span></dt><dd>
     see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
+</dd><dt><span class="term">
+<span class="strong"><strong>--threads</strong></span> <span class="emphasis"><em>INT</em></span>
+</span></dt><dd>
+    see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
 </dd></dl></div></div><div class="refsect3" title="Input/output options:"><a id="_input_output_options"></a><h4>Input/output options:</h4><div class="variablelist"><dl><dt><span class="term">
 <span class="strong"><strong>-A, --keep-alts</strong></span>
 </span></dt><dd>
@@ -354,13 +524,13 @@ demand. The original calling model can be invoked with the <span class="strong">
     minimum per-sample depth required to include a site in the non-variant
     block.
 </dd><dt><span class="term">
-<span class="strong"><strong>-M, --keep-masked-ref</strong></span>
+<span class="strong"><strong>-i, --insert-missed</strong></span> <span class="emphasis"><em>INT</em></span>
 </span></dt><dd>
-    output sites where REF allele is N
+    output also sites missed by mpileup but present in <span class="strong"><strong>-T, --targets-file</strong></span>.
 </dd><dt><span class="term">
-<span class="strong"><strong>-o, --output</strong></span> <span class="emphasis"><em>FILE</em></span>
+<span class="strong"><strong>-M, --keep-masked-ref</strong></span>
 </span></dt><dd>
-    see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
+    output sites where REF allele is N
 </dd><dt><span class="term">
 <span class="strong"><strong>-V, --skip-variants</strong></span> <span class="emphasis"><em>snps</em></span>|<span class="emphasis"><em>indels</em></span>
 </span></dt><dd>
@@ -433,11 +603,19 @@ the <span class="strong"><strong>-a, --allow-overlaps</strong></span> option is
 </span></dt><dd>
     First coordinate of the next file can precede last record of the current file.
 </dd><dt><span class="term">
-<span class="strong"><strong>-D, --remove-duplicates</strong></span>
+<span class="strong"><strong>-c, --compact-PS</strong></span>
 </span></dt><dd>
-    If a record is present in multiple files, output only the first instance.
+    Do not output PS tag at each site, only at the start of a new phase set block.
+</dd><dt><span class="term">
+<span class="strong"><strong>-d, --rm-dups</strong></span> <span class="emphasis"><em>snps</em></span>|<span class="emphasis"><em>indels</em></span>|<span class="emphasis"><em>both</em></span>|<span class="emphasis"><em>all</em></span>|<span class="emphasis"><em>none</em></span>
+</span></dt><dd>
+    Output duplicate records of specified type present in multiple files only once.
     Requires <span class="strong"><strong>-a, --allow-overlaps</strong></span>.
 </dd><dt><span class="term">
+<span class="strong"><strong>-D, --remove-duplicates</strong></span>
+</span></dt><dd>
+    Alias for <span class="strong"><strong>-d none</strong></span>
+</dd><dt><span class="term">
 <span class="strong"><strong>-f, --file-list</strong></span> <span class="emphasis"><em>FILE</em></span>
 </span></dt><dd>
     Read the list of files from a file.
@@ -465,6 +643,10 @@ the <span class="strong"><strong>-a, --allow-overlaps</strong></span> option is
 <span class="strong"><strong>-R, --regions-file</strong></span> <span class="emphasis"><em>FILE</em></span>
 </span></dt><dd>
     see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>. Requires <span class="strong"><strong>-a, --allow-overlaps</strong></span>.
+</dd><dt><span class="term">
+<span class="strong"><strong>--threads</strong></span> <span class="emphasis"><em>INT</em></span>
+</span></dt><dd>
+    see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
 </dd></dl></div></div><div class="refsect2" title="bcftools consensus [OPTIONS] FILE"><a id="consensus"></a><h3>bcftools consensus <span class="emphasis"><em>[OPTIONS]</em></span> <span class="emphasis"><em>FILE</em></span></h3><p>Create consensus sequence by applying VCF variants to a reference fasta file.</p><div class="variablelist"><dl><dt><span class="term">
 <span class="strong"><strong>-f, --fasta-ref</strong></span> <span class="emphasis"><em>FILE</em></span>
 </span></dt><dd>
@@ -539,6 +721,10 @@ the <span class="strong"><strong>-a, --allow-overlaps</strong></span> option is
 <span class="strong"><strong>-O, --output-type</strong></span> <span class="emphasis"><em>b</em></span>|<span class="emphasis"><em>u</em></span>|<span class="emphasis"><em>z</em></span>|<span class="emphasis"><em>v</em></span>
 </span></dt><dd>
     see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
+</dd><dt><span class="term">
+<span class="strong"><strong>--threads</strong></span> <span class="emphasis"><em>INT</em></span>
+</span></dt><dd>
+    see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
 </dd></dl></div></div><div class="refsect3" title="GEN/SAMPLE conversion:"><a id="_gen_sample_conversion"></a><h4>GEN/SAMPLE conversion:</h4><div class="variablelist"><dl><dt><span class="term">
 <span class="strong"><strong>-G, --gensample2vcf</strong></span> <span class="emphasis"><em>prefix</em></span> or <span class="emphasis"><em>gen-file</em></span>,<span class="emphasis"><em>sample-file</em></span>
 </span></dt><dd>
@@ -573,17 +759,41 @@ the <span class="strong"><strong>-a, --allow-overlaps</strong></span> option is
 </span></dt><dd>
     convert gVCF to VCF, expanding REF blocks into sites. Only sites
     with FILTER set to "PASS" or "." will be expanded.
+</dd><dt><span class="term">
+<span class="strong"><strong>-f, --fasta-ref</strong></span> <span class="emphasis"><em>file</em></span>
+</span></dt><dd>
+    reference sequence in fasta format. Must be indexed with samtools faidx
 </dd></dl></div></div><div class="refsect3" title="HAPS/SAMPLE conversion:"><a id="_haps_sample_conversion"></a><h4>HAPS/SAMPLE conversion:</h4><div class="variablelist"><dl><dt><span class="term">
 <span class="strong"><strong>--hapsample2vcf</strong></span> <span class="emphasis"><em>prefix</em></span> or <span class="emphasis"><em>haps-file</em></span>,<span class="emphasis"><em>sample-file</em></span>
 </span></dt><dd>
     convert from haps/sample format to VCF. The columns of .haps file are
     similar to .gen file above, but there are only two haplotype columns per
     sample. Note that the first column of the haps file is expected to be in
-    the form "CHR:POS_REF_ALT", for example:
+    the form "CHR:POS_REF_ALT(_END)?", with the _END being optional for
+    defining the INFO/END tag when ALT is a symbolic allele, for example:
 </dd></dl></div><pre class="screen">  .haps
   ----
   1:111485207_G_A rsID1 111485207 G A 0 1 0 0
-  1:111494194_C_T rsID2 111494194 C T 0 1 0 0</pre></div><div class="refsect3" title="HAPS/LEGEND/SAMPLE conversion:"><a id="_haps_legend_sample_conversion"></a><h4>HAPS/LEGEND/SAMPLE conversion:</h4><div class="variablelist"><dl><dt><span class="term">
+  1:111494194_C_T rsID2 111494194 C T 0 1 0 0
+  1:111495231_A_<DEL>_111495784 rsID3 111495231 A <DEL> 0 0 1 0</pre><div class="variablelist"><dl><dt><span class="term">
+<span class="strong"><strong>--hapsample</strong></span> <span class="emphasis"><em>prefix</em></span> or <span class="emphasis"><em>haps-file</em></span>,<span class="emphasis"><em>sample-file</em></span>
+</span></dt><dd>
+    convert from VCF to haps/sample format used by IMPUTE2 and SHAPEIT.
+    The columns of .haps file begin with ID,RSID,POS,REF,ALT. In order to
+    prevent strand swaps, the program uses IDs of the form
+    "CHROM:POS_REF_ALT".
+</dd><dt><span class="term">
+<span class="strong"><strong>--haploid2diploid</strong></span>
+</span></dt><dd>
+    with <span class="strong"><strong>-h</strong></span> option converts haploid genotypes to homozygous diploid
+    genotypes. For example, the program will print <span class="emphasis"><em>0 0</em></span> instead of the
+    default <span class="emphasis"><em>0 -</em></span>. This is useful for programs which do not handle haploid
+    genotypes correctly.
+</dd><dt><span class="term">
+<span class="strong"><strong>--vcf-ids</strong></span>
+</span></dt><dd>
+    output VCF IDs instead of "CHROM:POS_REF_ALT" IDs
+</dd></dl></div></div><div class="refsect3" title="HAPS/LEGEND/SAMPLE conversion:"><a id="_haps_legend_sample_conversion"></a><h4>HAPS/LEGEND/SAMPLE conversion:</h4><div class="variablelist"><dl><dt><span class="term">
 <span class="strong"><strong>-H, --haplegendsample2vcf</strong></span> <span class="emphasis"><em>prefix</em></span> or <span class="emphasis"><em>haps-file</em></span>,<span class="emphasis"><em>legend-file</em></span>,<span class="emphasis"><em>sample-file</em></span>
 </span></dt><dd>
     convert from haps/legend/sample format used by IMPUTE2 to VCF, see
@@ -641,7 +851,7 @@ the <span class="strong"><strong>-a, --allow-overlaps</strong></span> option is
 </dd><dt><span class="term">
 <span class="strong"><strong>-f, --fasta-ref</strong></span> <span class="emphasis"><em>file</em></span>
 </span></dt><dd>
-    reference sequence in fasta format
+    reference sequence in fasta format. Must be indexed with samtools faidx
 </dd><dt><span class="term">
 <span class="strong"><strong>-s, --samples</strong></span> <span class="emphasis"><em>LIST</em></span>
 </span></dt><dd>
@@ -867,10 +1077,10 @@ in the other files.</p><div class="variablelist"><dl><dt><span class="term">
     include only sites for which <span class="emphasis"><em>EXPRESSION</em></span> is true. See discussion
     of <span class="strong"><strong>-e, --exclude</strong></span> above.
 </dd><dt><span class="term">
-<span class="strong"><strong>-n, --nfiles</strong></span> [+-=]<span class="emphasis"><em>INT</em></span>
+<span class="strong"><strong>-n, --nfiles</strong></span> [+-=]<span class="emphasis"><em>INT</em></span>|~<span class="emphasis"><em>BITMAP</em></span>
 </span></dt><dd>
-    output positions present in this many (=), this many or more (+), or this
-    many or fewer (-) files
+    output positions present in this many (=), this many or more (+), this
+    many or fewer (-), or the exact same (~) files
 </dd><dt><span class="term">
 <span class="strong"><strong>-o, --output</strong></span> <span class="emphasis"><em>FILE</em></span>
 </span></dt><dd>
@@ -905,7 +1115,7 @@ in the other files.</p><div class="variablelist"><dl><dt><span class="term">
 </span></dt><dd>
     list of input files to output given as 1-based indices. With <span class="strong"><strong>-p</strong></span> and no
     <span class="strong"><strong>-w</strong></span>, all files are written.
-</dd></dl></div><div class="refsect3" title="Examples:"><a id="_examples"></a><h4>Examples:</h4><p>Create intersection and complements of two sets saving the output in dir/*</p><pre class="screen">    bcftools isec -p dir A.vcf.gz B.vcf.gz</pre><p>Filter sites in A and B (but not in C) and create intersection</p><pre class="screen">    bcftools isec -e'MAF<0.01' -i'dbSNP=1' -e- A.vcf.gz B.vcf.gz C.vcf.gz -p dir</pre><p>Extract and write records from A shared by both A and B using exac [...]
+</dd></dl></div><div class="refsect3" title="Examples:"><a id="_examples"></a><h4>Examples:</h4><p>Create intersection and complements of two sets saving the output in dir/*</p><pre class="screen">    bcftools isec -p dir A.vcf.gz B.vcf.gz</pre><p>Filter sites in A and B (but not in C) and create intersection</p><pre class="screen">    bcftools isec -e'MAF<0.01' -i'dbSNP=1' -e- A.vcf.gz B.vcf.gz C.vcf.gz -p dir</pre><p>Extract and write records from A shared by both A and B using exac [...]
 multi-sample file.  For example, when merging file <span class="emphasis"><em>A.vcf.gz</em></span> containing
 samples <span class="emphasis"><em>S1</em></span>, <span class="emphasis"><em>S2</em></span> and <span class="emphasis"><em>S3</em></span> and file <span class="emphasis"><em>B.vcf.gz</em></span> containing samples <span class="emphasis"><em>S3</em></span> and
 <span class="emphasis"><em>S4</em></span>, the output file will contain four samples named <span class="emphasis"><em>S1</em></span>, <span class="emphasis"><em>S2</em></span>, <span class="emphasis"><em>S3</em></span>, <span class="emphasis"><em>2:S3</em></span>
@@ -936,7 +1146,11 @@ For "vertical" merge take a look at <span class="strong"><strong><a class="link"
 <span class="strong"><strong>-i, --info-rules</strong></span> <span class="emphasis"><em>-</em></span>|<span class="emphasis"><em>TAG:METHOD</em></span>[,…]
 </span></dt><dd>
     Rules for merging INFO fields (scalars or vectors) or <span class="emphasis"><em>-</em></span> to disable the
-    default rules.  <span class="emphasis"><em>METHOD</em></span> is one of <span class="emphasis"><em>sum</em></span>, <span class="emphasis"><em>avg</em></span>, <span class="emphasis"><em>min</em></span>, <span class="emphasis"><em>max</em></span>, <span class="emphasis"><em>join</em></span>.
+    default rules. <span class="emphasis"><em>METHOD</em></span> is one of <span class="emphasis"><em>sum</em></span>, <span class="emphasis"><em>avg</em></span>, <span class="emphasis"><em>min</em></span>, <span class="emphasis"><em>max</em></span>, <span class="emphasis"><em>join</em></span>.
+    Default is <span class="emphasis"><em>DP:sum,DP4:sum</em></span> if these fields exist in the input files.
+    Fields with no specified rule will take the value from the first input file.
+    The merged QUAL value is currently set to the maximum. This behaviour is
+    not user controllable at the moment.
 </dd><dt><span class="term">
 <span class="strong"><strong>-l, --file-list</strong></span> <span class="emphasis"><em>FILE</em></span>
 </span></dt><dd>
@@ -966,16 +1180,38 @@ For "vertical" merge take a look at <span class="strong"><strong><a class="link"
 <span class="strong"><strong>-R, --regions-file</strong></span> <span class="emphasis"><em>file</em></span>
 </span></dt><dd>
     see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
-</dd></dl></div></div><div class="refsect2" title="bcftools norm [OPTIONS] file.vcf.gz"><a id="norm"></a><h3>bcftools norm [<span class="emphasis"><em>OPTIONS</em></span>] <span class="emphasis"><em>file.vcf.gz</em></span></h3><p>Left-align and normalize indels,  check if REF alleles match the reference,
+</dd><dt><span class="term">
+<span class="strong"><strong>--threads</strong></span> <span class="emphasis"><em>INT</em></span>
+</span></dt><dd>
+    see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
+</dd></dl></div></div><div class="refsect2" title="bcftools norm [OPTIONS] file.vcf.gz"><a id="norm"></a><h3>bcftools norm [<span class="emphasis"><em>OPTIONS</em></span>] <span class="emphasis"><em>file.vcf.gz</em></span></h3><p>Left-align and normalize indels, check if REF alleles match the reference,
 split multiallelic sites into multiple rows; recover multiallelics from
-multiple rows.</p><div class="variablelist"><dl><dt><span class="term">
+multiple rows. Left-alignment and normalization will only be applied if
+the <span class="strong"><strong><a class="link" href="#fasta_ref">--fasta-ref</a></strong></span> option is supplied.</p><div class="variablelist"><dl><dt><span class="term">
+<span class="strong"><strong>-c, --check-ref</strong></span> <span class="emphasis"><em>e</em></span>|<span class="emphasis"><em>w</em></span>|<span class="emphasis"><em>x</em></span>|<span class="emphasis"><em>s</em></span>
+</span></dt><dd>
+    what to do when incorrect or missing REF allele is encountered:
+    exit (<span class="emphasis"><em>e</em></span>), warn (<span class="emphasis"><em>w</em></span>), exclude (<span class="emphasis"><em>x</em></span>), or set/fix (<span class="emphasis"><em>s</em></span>) bad sites.
+    The <span class="emphasis"><em>w</em></span> option can be combined with <span class="emphasis"><em>x</em></span> and <span class="emphasis"><em>s</em></span>. Note that <span class="emphasis"><em>s</em></span>
+    can swap alleles and will update genotypes (GT) and AC counts,
+    but will not attempt to fix PL or other fields.
+</dd><dt><span class="term">
+<span class="strong"><strong>-d, --rm-dup</strong></span> <span class="emphasis"><em>snps</em></span>|<span class="emphasis"><em>indels</em></span>|<span class="emphasis"><em>both</em></span>|<span class="emphasis"><em>all</em></span>|<span class="emphasis"><em>none</em></span>
+</span></dt><dd>
+    If a record is present in multiple files, output only the first instance,
+    see <span class="strong"><strong>--collapse</strong></span> in <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>.
+    Requires <span class="strong"><strong>-a, --allow-overlaps</strong></span>.
+</dd><dt><span class="term">
 <span class="strong"><strong>-D, --remove-duplicates</strong></span>
 </span></dt><dd>
-    remove duplicate lines of the same type
+    If a record is present in multiple files, output only the first instance.
+    Alias for <span class="strong"><strong>-d none</strong></span>.  Requires <span class="strong"><strong>-a, --allow-overlaps</strong></span>.
 </dd><dt><span class="term">
-<span class="strong"><strong>-f, --fasta-ref</strong></span> <span class="emphasis"><em>FILE</em></span>
+<span class="strong"><strong>-f, --fasta-ref</strong></span> <span class="emphasis"><em>FILE</em></span><a id="fasta_ref"></a>
 </span></dt><dd>
-    reference sequence
+    reference sequence. Supplying this option will turn on left-alignment
+    and normalization, however, see also the <span class="strong"><strong><a class="link" href="#do_not_normalize">--do-not-normalize</a></strong></span>
+    option below.
 </dd><dt><span class="term">
 <span class="strong"><strong>-m, --multiallelics</strong></span> ←|+>[<span class="emphasis"><em>snps</em></span>|<span class="emphasis"><em>indels</em></span>|<span class="emphasis"><em>both</em></span>|<span class="emphasis"><em>any</em></span>]
 </span></dt><dd>
@@ -987,6 +1223,12 @@ multiple rows.</p><div class="variablelist"><dl><dt><span class="term">
     <span class="emphasis"><em>both</em></span>; if SNPs and indels should be merged into a single record, specify
     <span class="emphasis"><em>any</em></span>.
 </dd><dt><span class="term">
+<span class="strong"><strong>-N, --do-not-normalize</strong></span><a id="do_not_normalize"></a>
+</span></dt><dd>
+    the <span class="emphasis"><em>-c s</em></span> option can be used to fix or set the REF allele from the
+    reference <span class="emphasis"><em>-f</em></span>. The <span class="emphasis"><em>-N</em></span> option will not turn on indel normalisation
+    as the <span class="emphasis"><em>-f</em></span> option normally implies
+</dd><dt><span class="term">
 <span class="strong"><strong>-o, --output</strong></span> <span class="emphasis"><em>FILE</em></span>
 </span></dt><dd>
     see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
@@ -1015,11 +1257,15 @@ multiple rows.</p><div class="variablelist"><dl><dt><span class="term">
 </span></dt><dd>
     see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
 </dd><dt><span class="term">
+<span class="strong"><strong>--threads</strong></span> <span class="emphasis"><em>INT</em></span>
+</span></dt><dd>
+    see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
+</dd><dt><span class="term">
 <span class="strong"><strong>-w, --site-win</strong></span> <span class="emphasis"><em>INT</em></span>
 </span></dt><dd>
     maximum distance between two records to consider when locally
     sorting variants which changed position during the realignment
-</dd></dl></div></div><div class="refsect2" title="bcftools plugin NAME [OPTIONS] FILE — [PLUGIN OPTIONS]"><a id="plugin"></a><h3>bcftools plugin <span class="emphasis"><em>NAME</em></span> <span class="emphasis"><em>[OPTIONS]</em></span> <span class="emphasis"><em>FILE</em></span> — <span class="emphasis"><em>[PLUGIN OPTIONS]</em></span></h3><div class="refsect3" title="VCF input options:"><a id="_vcf_input_options_2"></a><h4>VCF input options:</h4><div class="variablelist"><dl><dt><spa [...]
+</dd></dl></div></div><div class="refsect2" title="bcftools [plugin NAME|+NAME] [OPTIONS] FILE — [PLUGIN OPTIONS]"><a id="plugin"></a><h3>bcftools [plugin <span class="emphasis"><em>NAME</em></span>|+<span class="emphasis"><em>NAME</em></span>] <span class="emphasis"><em>[OPTIONS]</em></span> <span class="emphasis"><em>FILE</em></span> — <span class="emphasis"><em>[PLUGIN OPTIONS]</em></span></h3><div class="refsect3" title="VCF input options:"><a id="_vcf_input_options_2"></a><h4>VCF in [...]
 <span class="strong"><strong>-e, --exclude</strong></span> <span class="emphasis"><em>EXPRESSION</em></span>
 </span></dt><dd>
     exclude sites for which <span class="emphasis"><em>EXPRESSION</em></span> is true. For valid expressions see
@@ -1053,21 +1299,33 @@ multiple rows.</p><div class="variablelist"><dl><dt><span class="term">
 <span class="strong"><strong>-O, --output-type</strong></span> <span class="emphasis"><em>b</em></span>|<span class="emphasis"><em>u</em></span>|<span class="emphasis"><em>z</em></span>|<span class="emphasis"><em>v</em></span>
 </span></dt><dd>
     see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
+</dd><dt><span class="term">
+<span class="strong"><strong>--threads</strong></span> <span class="emphasis"><em>INT</em></span>
+</span></dt><dd>
+    see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
 </dd></dl></div></div><div class="refsect3" title="Plugin options:"><a id="_plugin_options"></a><h4>Plugin options:</h4><div class="variablelist"><dl><dt><span class="term">
 <span class="strong"><strong>-h, --help</strong></span>
 </span></dt><dd>
     list plugin’s options
 </dd><dt><span class="term">
 <span class="strong"><strong>-l, --list-plugins</strong></span>
-</span></dt><dd>
-    List all available plugins. If not installed systemwide, set the environment
-    variable LD_LIBRARY_PATH (linux) or DYLD_LIBRARY_PATH (Mac OS X) to include
-    directory where <span class="strong"><strong>libhts.so</strong></span> is located.  The BCFTOOLS_PLUGINS
-    environment variable tells the program which directories to search.
-</dd><dt><span class="term">
+</span></dt><dd><p class="simpara">
+    List all available plugins.
+</p><p class="simpara">By default, appropriate system directories are searched for installed plugins.
+    You can override this by setting the BCFTOOLS_PLUGINS environment variable
+    to a colon-separated list of directories to search.
+    If BCFTOOLS_PLUGINS begins with a colon, ends with a colon, or contains
+    adjacent colons, the system directories are also searched at that position
+    in the list of directories.</p><p class="simpara">If htslib is not installed systemwide, set the environment variable
+    LD_LIBRARY_PATH (linux) or DYLD_LIBRARY_PATH (Mac OS X) to include the
+    directory where <span class="strong"><strong>libhts.so.1</strong></span> is located.</p></dd><dt><span class="term">
 <span class="strong"><strong>-v, --verbose</strong></span>
 </span></dt><dd>
     print debugging information to debug plugin failure
+</dd><dt><span class="term">
+<span class="strong"><strong>-V, --version</strong></span>
+</span></dt><dd>
+    print version string and exit
 </dd></dl></div></div><div class="refsect3" title="List of plugins coming with the distribution:"><a id="_list_of_plugins_coming_with_the_distribution"></a><h4>List of plugins coming with the distribution:</h4><div class="variablelist"><dl><dt><span class="term">
 <span class="strong"><strong>counts</strong></span>
 </span></dt><dd>
@@ -1107,9 +1365,13 @@ bcftools plugin
 # List available plugins
 bcftools plugin -l
 
-# One can run plugins in several ways
+# Run a plugin
 bcftools plugin counts in.vcf
+
+# Run a plugin using the abbreviated "+" notation
 bcftools +counts in.vcf
+
+# The input VCF can be streamed just like in other commands
 cat in.vcf | bcftools +counts
 
 # Print usage information of plugin "dosage"
@@ -1147,7 +1409,71 @@ int init(int argc, char **argv, bcf_hdr_t *in_hdr, bcf_hdr_t *out_hdr);
 bcf1_t *process(bcf1_t *rec);
 
 // Called after all lines have been processed to clean up
-void destroy(void);</pre></div></div><div class="refsect2" title="bcftools query [OPTIONS] file.vcf.gz [file.vcf.gz […]]"><a id="query"></a><h3>bcftools query [<span class="emphasis"><em>OPTIONS</em></span>] <span class="emphasis"><em>file.vcf.gz</em></span> [<span class="emphasis"><em>file.vcf.gz</em></span> […]]</h3><p>Extracts fields from VCF or BCF files and outputs them in user-defined format.</p><div class="variablelist"><dl><dt><span class="term">
+void destroy(void);</pre></div></div><div class="refsect2" title="bcftools polysomy [OPTIONS] file.vcf.gz"><a id="polysomy"></a><h3>bcftools polysomy [<span class="emphasis"><em>OPTIONS</em></span>] <span class="emphasis"><em>file.vcf.gz</em></span></h3><p>Detect number of chromosomal copies in VCFs annotates with the Illumina’s
+B-allele frequency (BAF) values. Note that this command is not compiled
+in by default, see the section <span class="strong"><strong>Optional Compilation with GSL</strong></span> in the INSTALL
+file for help.</p><div class="refsect3" title="General options:"><a id="_general_options_2"></a><h4>General options:</h4><div class="variablelist"><dl><dt><span class="term">
+<span class="strong"><strong>-o, --output-dir</strong></span> <span class="emphasis"><em>path</em></span>
+</span></dt><dd>
+    output directory
+</dd><dt><span class="term">
+<span class="strong"><strong>-r, --regions</strong></span> <span class="emphasis"><em>chr</em></span>|<span class="emphasis"><em>chr:pos</em></span>|<span class="emphasis"><em>chr:from-to</em></span>|<span class="emphasis"><em>chr:from-</em></span>[,…]
+</span></dt><dd>
+    see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
+</dd><dt><span class="term">
+<span class="strong"><strong>-R, --regions-file</strong></span> <span class="emphasis"><em>file</em></span>
+</span></dt><dd>
+    see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
+</dd><dt><span class="term">
+<span class="strong"><strong>-s, --sample</strong></span> <span class="emphasis"><em>string</em></span>
+</span></dt><dd>
+    samply name
+</dd><dt><span class="term">
+<span class="strong"><strong>-t, --targets</strong></span> <span class="emphasis"><em>LIST</em></span>
+</span></dt><dd>
+    see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
+</dd><dt><span class="term">
+<span class="strong"><strong>-T, --targets-file</strong></span> <span class="emphasis"><em>FILE</em></span>
+</span></dt><dd>
+    see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
+</dd><dt><span class="term">
+<span class="strong"><strong>-v, --verbose</strong></span>
+</span></dt><dd>
+    verbose debugging output which gives hints about the thresholds and decisions made
+    by the program. Note that the exact output can change between versions.
+</dd></dl></div></div><div class="refsect3" title="Algorithm options:"><a id="_algorithm_options"></a><h4>Algorithm options:</h4><div class="variablelist"><dl><dt><span class="term">
+<span class="strong"><strong>-b, --peak-size</strong></span> <span class="emphasis"><em>float</em></span>
+</span></dt><dd>
+    the minimum peak size considered as a good match can be from the interval [0,1]
+    where larger is stricter
+</dd><dt><span class="term">
+<span class="strong"><strong>-c, --cn-penalty</strong></span> <span class="emphasis"><em>float</em></span>
+</span></dt><dd>
+    a penalty for increasing copy number state. How this works: multiple peaks
+    are always a better fit than a single peak, therefore the program prefers
+    a single peak (normal copy number) unless the absolute deviation of the
+    multiple peaks fit is significantly smaller. Here the meaning of
+    "significant" is given by the <span class="emphasis"><em>float</em></span> from the interval [0,1] where
+    larger is stricter.
+</dd><dt><span class="term">
+<span class="strong"><strong>-f, --fit-th</strong></span> <span class="emphasis"><em>float</em></span>
+</span></dt><dd>
+    threshold for goodness of fit (normalized absolute deviation), smaller is stricter
+</dd><dt><span class="term">
+<span class="strong"><strong>-i, --include-aa</strong></span>
+</span></dt><dd>
+    include also the AA peak in CN2 and CN3 evaluation. This usually requires increasing <span class="strong"><strong>-f</strong></span>.
+</dd><dt><span class="term">
+<span class="strong"><strong>-m, --min-fraction</strong></span> <span class="emphasis"><em>float</em></span>
+</span></dt><dd>
+    minimum distinguishable fraction of aberrant cells. The experience shows that trustworthy
+    are estimates of 20% and more.
+</dd><dt><span class="term">
+<span class="strong"><strong>-p, --peak-symmetry</strong></span> <span class="emphasis"><em>float</em></span>
+</span></dt><dd>
+    a heuristics to filter failed fits where the expected peak symmetry is violated.
+    The <span class="emphasis"><em>float</em></span> is from the interval [0,1] and larger is stricter
+</dd></dl></div></div></div><div class="refsect2" title="bcftools query [OPTIONS] file.vcf.gz [file.vcf.gz […]]"><a id="query"></a><h3>bcftools query [<span class="emphasis"><em>OPTIONS</em></span>] <span class="emphasis"><em>file.vcf.gz</em></span> [<span class="emphasis"><em>file.vcf.gz</em></span> […]]</h3><p>Extracts fields from VCF or BCF files and outputs them in user-defined format.</p><div class="variablelist"><dl><dt><span class="term">
 <span class="strong"><strong>-c, --collapse</strong></span> <span class="emphasis"><em>snps</em></span>|<span class="emphasis"><em>indels</em></span>|<span class="emphasis"><em>both</em></span>|<span class="emphasis"><em>all</em></span>|<span class="emphasis"><em>some</em></span>|<span class="emphasis"><em>none</em></span>
 </span></dt><dd>
     see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
@@ -1202,6 +1528,11 @@ void destroy(void);</pre></div></div><div class="refsect2" title="bcftools query
 </span></dt><dd>
     see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
 </dd><dt><span class="term">
+<span class="strong"><strong>-u, --allow-undef-tags</strong></span>
+</span></dt><dd>
+    do not throw an error if there are undefined tags in the format string,
+    print "." instead
+</dd><dt><span class="term">
 <span class="strong"><strong>-v, --vcf-list</strong></span> <span class="emphasis"><em>FILE</em></span>
 </span></dt><dd>
     process multiple VCFs listed in the file
@@ -1244,15 +1575,18 @@ Emission probabilities:
 Transition probabilities:
   tAZ = P(AZ|HW)  .. from HW to AZ, the -a parameter
   tHW = P(HW|AZ)  .. from AZ to HW, the -H parameter
-  P(AZ|AZ) = 1 - P(HW|AZ) = 1 - tHW
-  P(HW|HW) = 1 - P(AZ|HW) = 1 - tAZ
 
   ci  = P_i(C)  .. probability of cross-over at site i, from genetic map
   AZi = P_i(AZ) .. probability of site i being AZ/non-AZ, scaled so that AZi+HWi = 1
   HWi = P_i(HW)
 
-  P_{i+1}(AZ) = oAZ * max[(1-tHW) * (1-ci) * AZ{i-1} , tAZ * ci * (1-AZ{i-1})]
-  P_{i+1}(HW) = oHW * max[(1-tAZ) * (1-ci) * (1-AZ{i-1}) , tHW * ci * AZ{i-1}]</pre></div><div class="refsect3" title="General Options:"><a id="_general_options"></a><h4>General Options:</h4><div class="variablelist"><dl><dt><span class="term">
+  P_{i+1}(AZ) = oAZ * max[(1 - tAZ * ci) * AZ{i-1} , tAZ * ci * (1-AZ{i-1})]
+  P_{i+1}(HW) = oHW * max[(1 - tHW * ci) * (1-AZ{i-1}) , tHW * ci * AZ{i-1}]</pre></div><div class="refsect3" title="General Options:"><a id="_general_options_3"></a><h4>General Options:</h4><div class="variablelist"><dl><dt><span class="term">
+<span class="strong"><strong>--AF-dflt</strong></span> <span class="emphasis"><em>FLOAT</em></span>
+</span></dt><dd>
+    in case allele frequency is not known, use the <span class="emphasis"><em>FLOAT</em></span>. By default, sites where
+    allele frequency cannot be determined, or is 0, are skipped.
+</dd><dt><span class="term">
 <span class="strong"><strong>--AF-tag</strong></span> <span class="emphasis"><em>TAG</em></span>
 </span></dt><dd>
     use the specified INFO tag <span class="emphasis"><em>TAG</em></span> as an allele frequency estimate
@@ -1290,6 +1624,10 @@ Transition probabilities:
     third column are used (position and Genetic_Map(cM)). The <span class="emphasis"><em>FILE</em></span> can
     chromosome name.
 </dd><dt><span class="term">
+<span class="strong"><strong>-M, --rec-rate</strong></span> <span class="emphasis"><em>FLOAT</em></span>
+</span></dt><dd>
+    constant recombination rate per bp
+</dd><dt><span class="term">
 <span class="strong"><strong>-r, --regions</strong></span> <span class="emphasis"><em>chr</em></span>|<span class="emphasis"><em>chr:pos</em></span>|<span class="emphasis"><em>chr:from-to</em></span>|<span class="emphasis"><em>chr:from-</em></span>[,…]
 </span></dt><dd>
     see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
@@ -1309,7 +1647,7 @@ Transition probabilities:
 <span class="strong"><strong>-T, --targets-file</strong></span> <span class="emphasis"><em>file</em></span>
 </span></dt><dd>
     see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
-</dd></dl></div></div><div class="refsect3" title="HMM Options:"><a id="_hmm_options"></a><h4>HMM Options:</h4><div class="variablelist"><dl><dt><span class="term">
+</dd></dl></div></div><div class="refsect3" title="HMM Options:"><a id="_hmm_options_2"></a><h4>HMM Options:</h4><div class="variablelist"><dl><dt><span class="term">
 <span class="strong"><strong>-a, --hw-to-az</strong></span> <span class="emphasis"><em>FLOAT</em></span>
 </span></dt><dd>
     P(AZ|HW) transition probability from AZ (autozygous) to HW (Hardy-Weinberg) state
@@ -1328,7 +1666,7 @@ default only sites are compared, <span class="strong"><strong>-s</strong></span>
 columns.</p><div class="variablelist"><dl><dt><span class="term">
 <span class="strong"><strong>-1, --1st-allele-only</strong></span>
 </span></dt><dd>
-    consider only 1st allele at multiallelic sites
+    consider only the 1st alternate allele at multiallelic sites
 </dd><dt><span class="term">
 <span class="strong"><strong>-c, --collapse</strong></span> <span class="emphasis"><em>snps</em></span>|<span class="emphasis"><em>indels</em></span>|<span class="emphasis"><em>both</em></span>|<span class="emphasis"><em>all</em></span>|<span class="emphasis"><em>some</em></span>|<span class="emphasis"><em>none</em></span>
 </span></dt><dd>
@@ -1342,7 +1680,12 @@ columns.</p><div class="variablelist"><dl><dt><span class="term">
 </span></dt><dd>
     produce verbose per-site and per-sample output
 </dd><dt><span class="term">
-<span class="strong"><strong>-e, --exons</strong></span> <span class="emphasis"><em>file.gz</em></span>
+<span class="strong"><strong>-e, --exclude</strong></span> <span class="emphasis"><em>EXPRESSION</em></span>
+</span></dt><dd>
+    exclude sites for which <span class="emphasis"><em>EXPRESSION</em></span> is true. For valid expressions see
+    <span class="strong"><strong><a class="link" href="#expressions" title="EXPRESSIONS">EXPRESSIONS</a></strong></span>.
+</dd><dt><span class="term">
+<span class="strong"><strong>-E, --exons</strong></span> <span class="emphasis"><em>file.gz</em></span>
 </span></dt><dd>
     tab-delimited file with exons for indel frameshifts statistics. The columns
     of the file are CHR, FROM, TO, with 1-based, inclusive, positions. The file
@@ -1356,7 +1699,12 @@ columns.</p><div class="variablelist"><dl><dt><span class="term">
 </span></dt><dd>
     faidx indexed reference sequence file to determine INDEL context
 </dd><dt><span class="term">
-<span class="strong"><strong>-i, --split-by-ID</strong></span>
+<span class="strong"><strong>-i, --include</strong></span> <span class="emphasis"><em>EXPRESSION</em></span>
+</span></dt><dd>
+    include only sites for which <span class="emphasis"><em>EXPRESSION</em></span> is true. For valid expressions see
+    <span class="strong"><strong><a class="link" href="#expressions" title="EXPRESSIONS">EXPRESSIONS</a></strong></span>.
+</dd><dt><span class="term">
+<span class="strong"><strong>-I, --split-by-ID</strong></span>
 </span></dt><dd>
     collect stats separately for sites which have the ID column set ("known
     sites") or which do not have the ID column set ("novel sites").
@@ -1384,6 +1732,14 @@ columns.</p><div class="variablelist"><dl><dt><span class="term">
 <span class="strong"><strong>-T, --targets-file</strong></span> <span class="emphasis"><em>file</em></span>
 </span></dt><dd>
     see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
+</dd><dt><span class="term">
+<span class="strong"><strong>-u, --user-tstv</strong></span> <span class="emphasis"><em><TAG[:min:max:n]></em></span>
+</span></dt><dd>
+    collect Ts/Tv stats for any tag using the given binning [0:1:100]
+</dd><dt><span class="term">
+<span class="strong"><strong>-v, --verbose</strong></span>
+</span></dt><dd>
+    produce verbose per-site and per-sample output
 </dd></dl></div></div><div class="refsect2" title="bcftools view [OPTIONS] file.vcf.gz [REGION […]]"><a id="view"></a><h3>bcftools view [<span class="emphasis"><em>OPTIONS</em></span>] <span class="emphasis"><em>file.vcf.gz</em></span> [<span class="emphasis"><em>REGION</em></span> […]]</h3><p>View, subset and filter VCF or BCF files by position and filtering expression.
 Convert between VCF and BCF. Former <span class="strong"><strong>bcftools subset</strong></span>.</p><div class="refsect3" title="Output options"><a id="_output_options"></a><h4>Output options</h4><div class="variablelist"><dl><dt><span class="term">
 <span class="strong"><strong>-G, --drop-genotypes</strong></span>
@@ -1423,11 +1779,19 @@ Convert between VCF and BCF. Former <span class="strong"><strong>bcftools subset
 <span class="strong"><strong>-T, --targets-file</strong></span> <span class="emphasis"><em>file</em></span>
 </span></dt><dd>
     see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
+</dd><dt><span class="term">
+<span class="strong"><strong>--threads</strong></span> <span class="emphasis"><em>INT</em></span>
+</span></dt><dd>
+    see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
 </dd></dl></div></div><div class="refsect3" title="Subset options:"><a id="_subset_options"></a><h4>Subset options:</h4><div class="variablelist"><dl><dt><span class="term">
 <span class="strong"><strong>-a, --trim-alt-alleles</strong></span>
 </span></dt><dd>
     trim alternate alleles not seen in subset. Type A, G and R INFO and FORMAT fields will also be trimmed
 </dd><dt><span class="term">
+<span class="strong"><strong>--force-samples</strong></span>
+</span></dt><dd>
+    only warn about unknown subset samples
+</dd><dt><span class="term">
 <span class="strong"><strong>-I, --no-update</strong></span>
 </span></dt><dd>
     do not (re)calculate INFO fields for the subset (currently INFO/AC and INFO/AN)
@@ -1502,7 +1866,7 @@ Convert between VCF and BCF. Former <span class="strong"><strong>bcftools subset
 </span></dt><dd>
     exclude sites where all samples are phased
 </dd><dt><span class="term">
-<span class="strong"><strong>-q, --min-af</strong></span> <span class="emphasis"><em>FLOAT</em></span>[<span class="emphasis"><em>:nref</em></span>|<span class="emphasis"><em>:alt1</em></span>|<span class="emphasis"><em>:minor</em></span>|:'major'|:'nonmajor']
+<span class="strong"><strong>-q, --min-af</strong></span> <span class="emphasis"><em>FLOAT</em></span>[<span class="emphasis"><em>:nref</em></span>|<span class="emphasis"><em>:alt1</em></span>|<span class="emphasis"><em>:minor</em></span>|<span class="emphasis"><em>:major</em></span>|<span class="emphasis"><em>:nonmajor</em></span>]
 </span></dt><dd>
     minimum allele frequency (INFO/AC / INFO/AN) of sites to be printed.
     Specifying the type of allele is optional and can be set to
@@ -1510,7 +1874,7 @@ Convert between VCF and BCF. Former <span class="strong"><strong>bcftools subset
     frequent (<span class="emphasis"><em>minor</em></span>), the most frequent (<span class="emphasis"><em>major</em></span>) or sum of all but the
     most frequent (<span class="emphasis"><em>nonmajor</em></span>) alleles.
 </dd><dt><span class="term">
-<span class="strong"><strong>-Q, --max-af</strong></span> <span class="emphasis"><em>FLOAT</em></span>[<span class="emphasis"><em>:nref</em></span>|<span class="emphasis"><em>:alt1</em></span>|<span class="emphasis"><em>:minor</em></span>|:'major'|:'nonmajor']
+<span class="strong"><strong>-Q, --max-af</strong></span> <span class="emphasis"><em>FLOAT</em></span>[<span class="emphasis"><em>:nref</em></span>|<span class="emphasis"><em>:alt1</em></span>|<span class="emphasis"><em>:minor</em></span>|<span class="emphasis"><em>:major</em></span>|<span class="emphasis"><em>:nonmajor</em></span>]
 </span></dt><dd>
     maximum allele frequency (INFO/AC / INFO/AN) of sites to be printed.
     Specifying the type of allele is optional and can be set to
@@ -1528,20 +1892,28 @@ Convert between VCF and BCF. Former <span class="strong"><strong>bcftools subset
 </dd><dt><span class="term">
 <span class="strong"><strong>-v, --types</strong></span> <span class="emphasis"><em>snps</em></span>|<span class="emphasis"><em>indels</em></span>|<span class="emphasis"><em>mnps</em></span>|<span class="emphasis"><em>other</em></span>
 </span></dt><dd>
-    comma-separated list of variant types to select
+    comma-separated list of variant types to select. Site is selected if
+    any of the ALT alleles is of the type requested. Types are determined
+    by comparing the REF and ALT alleles in the VCF record not INFO tags
+    like INFO/INDEL or INFO/VT. Use <span class="strong"><strong>--include</strong></span> to select based on INFO
+    tags.
 </dd><dt><span class="term">
 <span class="strong"><strong>-V, --exclude-types</strong></span> <span class="emphasis"><em>snps</em></span>|<span class="emphasis"><em>indels</em></span>|<span class="emphasis"><em>mnps</em></span>|<span class="emphasis"><em>other</em></span>
 </span></dt><dd>
-    comma-separated list of variant types to exclude
+    comma-separated list of variant types to exclude. Site is excluded if
+    any of the ALT alleles is of the type requested. Types are determined
+    by comparing the REF and ALT alleles in the VCF record not INFO tags
+    like INFO/INDEL or INFO/VT. Use <span class="strong"><strong>--exclude</strong></span> to exclude based on INFO tags.
 </dd><dt><span class="term">
 <span class="strong"><strong>-x, --private</strong></span>
 </span></dt><dd>
-    print sites where only the subset samples carry an non-reference allele
+    print sites where only the subset samples carry an non-reference allele.
+    Requires <span class="strong"><strong>--samples</strong></span> or <span class="strong"><strong>--samples-file</strong></span>.
 </dd><dt><span class="term">
 <span class="strong"><strong>-X, --exclude-private</strong></span>
 </span></dt><dd>
     exclude sites where only the subset samples carry an non-reference allele
-</dd></dl></div></div></div></div><div class="refsect1" title="EXPRESSIONS"><a id="expressions"></a><h2>EXPRESSIONS</h2><p>These filtering expressions are accepted by <span class="strong"><strong><a class="link" href="#annotate" title="bcftools annotate [OPTIONS] FILE">annotate</a></strong></span>,
+</dd></dl></div></div></div><div class="refsect2" title="bcftools help [COMMAND] | bcftools --help [COMMAND]"><a id="help"></a><h3>bcftools help [<span class="emphasis"><em>COMMAND</em></span>] | bcftools --help [<span class="emphasis"><em>COMMAND</em></span>]</h3><p>Display  a  brief usage message listing the bcftools commands available.  If the name of a command is also given, e.g., bcftools help view, the detailed usage message for that particular command is displayed.</p></div><div c [...]
 <span class="strong"><strong><a class="link" href="#filter" title="bcftools filter [OPTIONS] FILE">filter</a></strong></span>, <span class="strong"><strong><a class="link" href="#query" title="bcftools query [OPTIONS] file.vcf.gz [file.vcf.gz […]]">query</a></strong></span> and <span class="strong"><strong><a class="link" href="#view" title="bcftools view [OPTIONS] file.vcf.gz [REGION […]]">view</a></strong></span> commands.</p><div class="itemizedlist" title="Valid expressions may conta [...]
 numerical constants, string constants, file names
 </p><pre class="literallayout">1, 1.0, 1e-4
@@ -1560,9 +1932,14 @@ logical operators
 INFO tags, FORMAT tags, column names
 </p><pre class="literallayout">INFO/DP or DP
 FORMAT/DV, FMT/DV, or DV
-FILTER, QUAL, ID, REF, ALT[0]</pre></li><li class="listitem"><p class="simpara">
+FILTER, QUAL, ID, POS, REF, ALT[0]</pre></li><li class="listitem"><p class="simpara">
 1 (or 0) to test the presence (or absence) of a flag
 </p><pre class="literallayout">FlagA=1 && FlagB=0</pre></li><li class="listitem"><p class="simpara">
+"." to test missing values
+</p><pre class="literallayout">DP=".", DP!=".", ALT="."</pre></li><li class="listitem"><p class="simpara">
+missing genotypes can be matched regardless of phase and ploidy (".|.", "./.", ".")
+using this expression
+</p><pre class="literallayout">GT="."</pre></li><li class="listitem"><p class="simpara">
 TYPE for variant type in REF,ALT columns (indel,snp,mnp,ref,other)
 </p><pre class="literallayout">TYPE="indel" | TYPE="snp"</pre></li><li class="listitem"><p class="simpara">
 array subscripts, "*" for any field
@@ -1585,7 +1962,7 @@ true for the string vector INFO/STR=AB,CD.
 Variables and function names are case-insensitive, but not tag names. For example,
 "qual" can be used instead of "QUAL", "strlen()" instead of "STRLEN()" , but
 not "dp" instead of "DP".
-</li></ul></div><p><span class="strong"><strong>Examples:</strong></span></p><pre class="literallayout">MIN(DV)>5</pre><pre class="literallayout">MIN(DV/DP)>0.3</pre><pre class="literallayout">MIN(DP)>10 & MIN(DV)>3</pre><pre class="literallayout">QUAL>10 |  FMT/GQ>10   .. selects only GQ>10 samples</pre><pre class="literallayout">QUAL>10 || FMT/GQ>10   .. selects all samples at QUAL>10 sites</pre><pre class="literallayout">TYPE="snp" && QUAL> [...]
+</li></ul></div><p><span class="strong"><strong>Examples:</strong></span></p><pre class="literallayout">MIN(DV)>5</pre><pre class="literallayout">MIN(DV/DP)>0.3</pre><pre class="literallayout">MIN(DP)>10 & MIN(DV)>3</pre><pre class="literallayout">FMT/DP>10  & FMT/GQ>10 .. both conditions must be satisfied within one sample</pre><pre class="literallayout">FMT/DP>10 && FMT/GQ>10 .. the conditions can be satisfied in different samples</pre><pre class [...]
 have special meaning in the shell.
 An example of expression enclosed in single quotes which cause
 that the whole expression is passed to the program as intended:</p><pre class="literallayout">bcftools view -i '%ID!="." & MAF[0]<0.01'</pre><p>Please refer to the documentation of your shell for details.</p></div><div class="refsect1" title="SCRIPTS AND OPTIONS"><a id="_scripts_and_options"></a><h2>SCRIPTS AND OPTIONS</h2><div class="refsect2" title="plot-vcfstats [OPTIONS] file.vchk […]"><a id="plot-vcfstats"></a><h3>plot-vcfstats [<span class="emphasis"><em>OPTIONS</em></span>] [...]
diff --git a/doc/bcftools.txt b/doc/bcftools.txt
index efb6c3d..e26692d 100644
--- a/doc/bcftools.txt
+++ b/doc/bcftools.txt
@@ -26,7 +26,7 @@ bcftools - utilities for variant calling and manipulating VCFs and BCFs.
 
 SYNOPSIS
 --------
-*bcftools* ['COMMAND'] ['OPTIONS']
+*bcftools* [--version|--version-only] [--help] ['COMMAND'] ['OPTIONS']
 
 
 DESCRIPTION
@@ -38,7 +38,8 @@ transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.
 Most commands accept VCF, bgzipped VCF and BCF with filetype detected
 automatically even when streaming from a pipe. Indexed VCF and BCF
 will work in all situations. Un-indexed VCF and BCF and streams will
-work in most, but not all situations.
+work in most, but not all situations. In general, whenever multiple VCFs are 
+read simultaneously, they must be indexed and therefore also compressed.
 
 BCFtools is designed to work on a stream. It regards an input file "-" as the
 standard input (stdin) and outputs to the standard output (stdout). Several
@@ -75,6 +76,7 @@ list of available options, run *bcftools* 'COMMAND' without arguments.
 
 - *<<annotate,annotate>>*   .. edit VCF files, add or remove annotations
 - *<<call,call>>*        ..  SNP/indel calling (former "view")
+- *<<cnv,cnv>>*          ..  Copy Number Variation caller
 - *<<concat,concat>>*    ..  concatenate VCF/BCF files from the same set of samples
 - *<<consensus,consensus>>*    ..  create consensus sequence by applying VCF variants
 - *<<convert,convert>>*  ..  convert VCF/BCF to other formats and back
@@ -85,6 +87,7 @@ list of available options, run *bcftools* 'COMMAND' without arguments.
 - *<<merge,merge>>*      ..  merge VCF/BCF files files from non-overlapping sample sets
 - *<<norm,norm>>*        ..  normalize indels
 - *<<plugin,plugin>>*    ..  run user-defined plugin
+- *<<polysomy,polysomy>>*   ..  detect contaminations and whole-chromosome aberrations
 - *<<query,query>>*      ..  transform VCF/BCF into user-defined formats
 - *<<reheader,reheader>>*   ..  modify VCF/BCF header, change sample names
 - *<<roh,roh>>*          ..  identify runs of homo/auto-zygosity
@@ -162,6 +165,9 @@ specific commands to see if they apply.
 
 *-O, --output-type* 'b'|'u'|'z'|'v'::
     Output compressed BCF ('b'), uncompressed BCF ('u'), compressed VCF ('z'), uncompressed VCF ('v').
+    Use the -Ou option when piping between bcftools subcommands to speed up
+    performance by removing unecessary compression/decompression and
+    VCF<-->BCF conversion.
 
 *-r, --regions* 'chr'|'chr:pos'|'chr:from-to'|'chr:from-'[,...]::
     Comma-separated list of regions, see also *-R, --regions-file*. Note
@@ -186,13 +192,44 @@ specific commands to see if they apply.
 *-s, --samples* \[^]'LIST'::
     Comma-separated list of samples to include or exclude if prefixed
     with "^".
+    Note that in general tags such as INFO/AC, INFO/AN, etc are not updated
+    to correspond to the subset samples. *<<view,bcftools view>>* is the
+    exception where some tags will be updated (unless the *-I, --no-update*
+    option is used; see *<<view,bcftools view>>* documentation). To use updated 
+    tags for the subset in another command one can pipe from *view* into
+    that command. For example:
+----
+    bcftools view -Ou -s sample1,sample2 file.vcf | bcftools query -f %INFO/AC\t%INFO/AN\n
+----
 
-*-S, --samples-file* [^]'FILE'::
+*-S, --samples-file* [^]'FILE'[[samples_file]]::
     File of sample names to include or exclude if prefixed with "^".
-    One sample per line.
+    One sample per line. See also the note above for the *-s, --samples*
+    option.
     The command *<<call,bcftools call>>* accepts an optional second
-    column indicating ploidy (0, 1 or 2) and can parse also PED files.
-    With *<<call,bcftools call>> -C* 'trio', PED file is expected.
+    column indicating ploidy (0, 1 or 2) or sex (as defined by
+    *<<ploidy,--ploidy>>*, for example "F" or "M"), and can parse also PED
+    files. If the second column is not present,
+    the sex "F" is assumed.
+    With *<<call,bcftools call>> -C* 'trio', PED file is expected. File
+    formats examples:
+----
+    sample1    1
+    sample2    2
+    sample3    2
+
+  or
+
+    sample1    M
+    sample2    F
+    sample3    F
+
+  or a .ped file (here is shown a minimum working example, the first column is 
+  ignored and the last indicates sex: 1=male, 2=female)
+
+    ignored daughterA fatherA motherA 2
+    ignored sonB fatherB motherB 1
+----
 
 *-t, --targets* \[^]'chr'|'chr:pos'|'chr:from-to'|'chr:from-'[,...]::
     Similar as *-r, --regions*, but the next position is accessed by streaming the
@@ -211,12 +248,18 @@ specific commands to see if they apply.
 
     ::
     With the *call -C* 'alleles' command, third column of the targets file must
-    be comma-separated list of alleles, starting with the reference allele.
+    be comma-separated list of alleles, starting with the reference allele. 
+    Note that the file must be compressed and index.
     Such a file can be easily created from a VCF using:
 ----
-    bcftools query -f'%CHROM\t%POS\t%REF,%ALT\n' file.vcf
+    bcftools query -f'%CHROM\t%POS\t%REF,%ALT\n' file.vcf | bgzip -c > als.tsv.gz && tabix -s1 -b2 -e2 als.tsv.gz
 ----
 
+*--threads* 'INT'::
+    Number of output compression threads to use in addition to main thread. 
+    Only used when '--output-type' is 'b' or 'z'. Default: 0.
+
+
 [[annotate]]
 === bcftools annotate '[OPTIONS]' 'FILE'
 
@@ -258,8 +301,11 @@ This command allows to add or remove annotations.
     can be edited, where INFO tags can be written both as "INFO/TAG" or simply "TAG",
     and FORMAT tags can be written as "FORMAT/TAG" or "FMT/TAG".
     To carry over all INFO annotations, use "INFO". To add all INFO annotations except
-    "TAG", use "^INFO/TAG". By default, existing values are replaced. To add
-    values without overwriting existing annotations, use "+TAG" instead of "TAG".
+    "TAG", use "^INFO/TAG". By default, existing values are replaced.
+    To add annotations without overwriting existing values (that is, to add missing tags or
+    add values to existing tags with missing values), use "+TAG" instead of "TAG".
+    To append to existing values (rather than replacing or leaving untouched), use "=TAG"
+    (instead of "TAG" or "+TAG").
     To replace only existing values without modifying missing annotations, use "-TAG".
     If the annotation file is not a VCF/BCF, all new annotations must be
     defined via *-h, --header-lines*.
@@ -288,6 +334,9 @@ This command allows to add or remove annotations.
     include only sites for which 'EXPRESSION' is true. For valid expressions see
     *<<expressions,EXPRESSIONS>>*.
 
+*-m, --mark-sites* [+-]'TAG'::
+    annotate sites which are present ("+") or absent ("-") in the *-a* file with a new INFO/TAG flag
+
 *-o, --output* 'FILE'::
     see *<<common_options,Common Options>>*
 
@@ -315,6 +364,9 @@ This command allows to add or remove annotations.
     given as "src_name dst_name\n", separated by whitespaces, each pair on a
     separate line.
 
+*--threads* 'INT'::
+    see *<<common_options,Common Options>>*
+
 *-x, --remove* 'list'::
     List of annotations to remove. Use "FILTER" to remove all filters or
     "FILTER/SomeFilter" to remove a specific filter. Similarly, "INFO" can
@@ -350,6 +402,91 @@ This command allows to add or remove annotations.
     bcftools annotate -a annots.bed.gz -h annots.hdr -c CHROM,FROM,TO,TAG input.vcf
 ----
 
+[[cnv]]
+=== bcftools cnv '[OPTIONS]' 'FILE'
+
+Copy number variation caller, requires a VCF annotated with the Illumina's
+B-allele frequency (BAF) and Log R Ratio intensity (LRR) values. The HMM
+considers the following copy number states: CN 2 (normal), 1 (single-copy
+loss), 0 (complete loss), 3 (single-copy gain).
+
+
+==== General Options:
+
+*-c, --control-sample* 'string'::
+    optional control sample name. If given, pairwise calling is performed
+    and the *-P*  option can be used
+
+*-f, --AF-file* 'file'::
+    read allele frequencies from  a tab-delimited file with the columns CHR,POS,REF,ALT,AF
+
+*-o, --output-dir 'path'::
+    output directory 
+
+*-p, --plot-threshold 'float'::
+    call *matplotlib* to produce plots for chromosomes with quality at least 'float',
+    useful for visual inspection of the calls. With *-p 0*, plots for all chromosomes will be 
+    generated. If not given, a *matplotlib* script will be created but not called.
+
+*-r, --regions* 'chr'|'chr:pos'|'chr:from-to'|'chr:from-'[,...]::
+    see *<<common_options,Common Options>>*
+
+*-R, --regions-file* 'file'::
+    see *<<common_options,Common Options>>*
+
+*-s, --query-sample* 'string'::
+    query samply name
+
+*-t, --targets* 'LIST'::
+    see *<<common_options,Common Options>>*
+
+*-T, --targets-file* 'FILE'::
+    see *<<common_options,Common Options>>*
+
+==== HMM Options:
+
+*-a, --aberrant* 'float'[,'float']::
+    fraction of aberrant cells in query and control. The hallmark of
+    duplications and contaminations is the BAF value of heterozygous markers
+    which is dependent on the fraction of aberrant cells. Sensitivity to
+    smaller fractions of cells can be increased by setting *-a* to a lower value. Note
+    however, that this comes at the cost of increased false discovery rate.
+
+*-b, --BAF-weight* 'float'::
+    relative contribution from BAF
+
+*d, --BAF-dev* 'float'[,'float']::
+    expected BAF deviation in query and control, i.e. the noise observed
+    in the data.
+
+*-e, --err-prob* 'float'::
+    uniform error probability
+
+*-l, --LRR-weight* 'float'::
+    relative contribution from LRR. With noisy data, this option can have big effect
+    on the number of calls produced. In truly random noise (such as in simulated data),
+    the value should be set high (1.0), but in the presence of systematic noise
+    when LRR are not informative, lower values result in cleaner calls (0.2).
+
+*-L, --LRR-smooth-win* 'int'::
+    reduce LRR noise by applying moving average given this window size
+
+*-O, --optimize* 'float'::
+    iteratively estimate the fraction of aberrant cells, down to the given fraction.
+    Lowering this value from the default 1.0 to say, 0.3, can help discover more
+    events but also increases noise
+
+*-P, --same-prob* 'float'::
+    the prior probability of the query and the control sample being the same.
+    Setting to 0 calls both independently, setting to 1 forces the same copy
+    number state in both.
+
+*-x, --xy-prob* 'float'::
+    the HMM probability of transition to another copy number state. Increasing this
+    values leads to smaller and more frequent calls.
+
+
+
 
 [[call]]
 === bcftools call '[OPTIONS]' 'FILE'
@@ -361,9 +498,34 @@ demand. The original calling model can be invoked with the *-c* option.
 
 ==== File format options:
 
+*-o, --output* 'FILE'::
+    see *<<common_options,Common Options>>*
+
 *-O, --output-type* 'b'|'u'|'z'|'v'::
     see *<<common_options,Common Options>>*
 
+*--ploidy* 'ASSEMBLY'['?'][[ploidy]]::
+    predefined ploidy, use 'list' (or any other unused word) to print a list
+    of all predefined assemblies. Append a question mark to print the actual
+    definition. See also *--ploidy-file*.
+
+*--ploidy-file* 'FILE'::
+    ploidy definition given as a space/tab-delimited list of
+    CHROM, FROM, TO, SEX, PLOIDY. The SEX codes are arbitrary and
+    correspond to the ones used by *<<samples_file,--samples-file>>*. 
+    The default ploidy can be given using the starred records (see
+    below), unlisted regions have ploidy 2. The default ploidy definition is
+----
+    X 1 60000 M 1
+    X 2699521 154931043 M 1
+    Y 1 59373566 M 1
+    Y 1 59373566 F 0
+    MT 1 16569 M 1
+    MT 1 16569 F 1
+    *  * *     M 2
+    *  * *     F 2
+----
+
 *-r, --regions* 'chr'|'chr:pos'|'chr:from-to'|'chr:from-'[,...]::
     see *<<common_options,Common Options>>*
 
@@ -382,6 +544,9 @@ demand. The original calling model can be invoked with the *-c* option.
 *-T, --targets-file* 'FILE'::
     see *<<common_options,Common Options>>*
 
+*--threads* 'INT'::
+    see *<<common_options,Common Options>>*
+
 ==== Input/output options:
 
 *-A, --keep-alts*::
@@ -398,12 +563,12 @@ demand. The original calling model can be invoked with the *-c* option.
     minimum per-sample depth required to include a site in the non-variant
     block.
 
+*-i, --insert-missed* 'INT'::
+    output also sites missed by mpileup but present in *-T, --targets-file*.
+
 *-M, --keep-masked-ref*::
     output sites where REF allele is N
 
-*-o, --output* 'FILE'::
-    see *<<common_options,Common Options>>*
-
 *-V, --skip-variants* 'snps'|'indels'::
     skip indel/SNP sites
 
@@ -470,10 +635,16 @@ the *-a, --allow-overlaps* option is specified.
 *-a, --allow-overlaps*::
     First coordinate of the next file can precede last record of the current file.
 
-*-D, --remove-duplicates*::
-    If a record is present in multiple files, output only the first instance.
+*-c, --compact-PS*::
+    Do not output PS tag at each site, only at the start of a new phase set block.
+
+*-d, --rm-dups* 'snps'|'indels'|'both'|'all'|'none'::
+    Output duplicate records of specified type present in multiple files only once.
     Requires *-a, --allow-overlaps*.
 
+*-D, --remove-duplicates*::
+    Alias for *-d none*
+
 *-f, --file-list* 'FILE'::
     Read the list of files from a file.
 
@@ -495,6 +666,9 @@ the *-a, --allow-overlaps* option is specified.
 *-R, --regions-file* 'FILE'::
     see *<<common_options,Common Options>>*. Requires *-a, --allow-overlaps*.
 
+*--threads* 'INT'::
+    see *<<common_options,Common Options>>*
+
 
 [[consensus]]
 === bcftools consensus '[OPTIONS]' 'FILE'
@@ -571,6 +745,9 @@ Create consensus sequence by applying VCF variants to a reference fasta file.
 *-O, --output-type* 'b'|'u'|'z'|'v'::
     see *<<common_options,Common Options>>*
 
+*--threads* 'INT'::
+    see *<<common_options,Common Options>>*
+
 ==== GEN/SAMPLE conversion:
 *-G, --gensample2vcf* 'prefix' or 'gen-file','sample-file'::
     convert IMPUTE2 output to VCF. The second column must be of the form
@@ -606,19 +783,39 @@ Create consensus sequence by applying VCF variants to a reference fasta file.
     convert gVCF to VCF, expanding REF blocks into sites. Only sites
     with FILTER set to "PASS" or "." will be expanded.
 
+*-f, --fasta-ref* 'file'::
+    reference sequence in fasta format. Must be indexed with samtools faidx
+
 ==== HAPS/SAMPLE conversion:
 *--hapsample2vcf* 'prefix' or 'haps-file','sample-file'::
     convert from haps/sample format to VCF. The columns of .haps file are
     similar to .gen file above, but there are only two haplotype columns per
     sample. Note that the first column of the haps file is expected to be in
-    the form "CHR:POS_REF_ALT", for example:
+    the form "CHR:POS_REF_ALT(_END)?", with the _END being optional for
+    defining the INFO/END tag when ALT is a symbolic allele, for example:
 ----
   .haps
   ----
   1:111485207_G_A rsID1 111485207 G A 0 1 0 0
   1:111494194_C_T rsID2 111494194 C T 0 1 0 0
+  1:111495231_A_<DEL>_111495784 rsID3 111495231 A <DEL> 0 0 1 0
 ----
 
+*--hapsample* 'prefix' or 'haps-file','sample-file'::
+    convert from VCF to haps/sample format used by IMPUTE2 and SHAPEIT.
+    The columns of .haps file begin with ID,RSID,POS,REF,ALT. In order to 
+    prevent strand swaps, the program uses IDs of the form 
+    "CHROM:POS_REF_ALT".
+
+*--haploid2diploid*::
+    with *-h* option converts haploid genotypes to homozygous diploid
+    genotypes. For example, the program will print '0 0' instead of the 
+    default '0 -'. This is useful for programs which do not handle haploid
+    genotypes correctly.
+
+*--vcf-ids*::
+    output VCF IDs instead of "CHROM:POS_REF_ALT" IDs
+
 ==== HAPS/LEGEND/SAMPLE conversion:
 *-H, --haplegendsample2vcf* 'prefix' or 'haps-file','legend-file','sample-file'::
     convert from haps/legend/sample format used by IMPUTE2 to VCF, see
@@ -674,7 +871,7 @@ Create consensus sequence by applying VCF variants to a reference fasta file.
     are not supported yet, missing data can be indicated with "--".
 
 *-f, --fasta-ref* 'file'::
-    reference sequence in fasta format
+    reference sequence in fasta format. Must be indexed with samtools faidx
 
 *-s, --samples* 'LIST'::
     list of sample names. See *<<common_options,Common Options>>*
@@ -900,9 +1097,9 @@ in the other files.
     include only sites for which 'EXPRESSION' is true. See discussion
     of *-e, --exclude* above.
 
-*-n, --nfiles* \[+-=]'INT'::
-    output positions present in this many (=), this many or more (+), or this
-    many or fewer (-) files
+*-n, --nfiles* \[+-=]'INT'|~'BITMAP'::
+    output positions present in this many (=), this many or more (+), this
+    many or fewer (-), or the exact same (~) files
 
 *-o, --output* 'FILE'::
     see *<<common_options,Common Options>>*.  When several files are being
@@ -952,6 +1149,11 @@ Extract records private to A or B comparing by position only
     bcftools isec -p dir -n-1 -c all A.vcf.gz B.vcf.gz
 ----
 
+Print a list of records which are present in A and B but not in C and D
+----
+    bcftools isec -n~1100 -c all A.vcf.gz B.vcf.gz C.vcf.gz D.vcf.gz
+----
+
 
 [[merge]]
 === bcftools merge ['OPTIONS'] 'A.vcf.gz' 'B.vcf.gz' [...]
@@ -987,7 +1189,11 @@ For "vertical" merge take a look at *<<norm,bcftools norm>>* instead.
 
 *-i, --info-rules* '-'|'TAG:METHOD'[,...]::
     Rules for merging INFO fields (scalars or vectors) or '-' to disable the
-    default rules.  'METHOD' is one of 'sum', 'avg', 'min', 'max', 'join'.
+    default rules. 'METHOD' is one of 'sum', 'avg', 'min', 'max', 'join'.
+    Default is 'DP:sum,DP4:sum' if these fields exist in the input files.
+    Fields with no specified rule will take the value from the first input file.
+    The merged QUAL value is currently set to the maximum. This behaviour is 
+    not user controllable at the moment.
 
 *-l, --file-list* 'FILE'::
     read file names from 'FILE'
@@ -1015,19 +1221,37 @@ For "vertical" merge take a look at *<<norm,bcftools norm>>* instead.
 *-R, --regions-file* 'file'::
     see *<<common_options,Common Options>>*
 
+*--threads* 'INT'::
+    see *<<common_options,Common Options>>*
 
 
 [[norm]]
 === bcftools norm ['OPTIONS'] 'file.vcf.gz'
-Left-align and normalize indels,  check if REF alleles match the reference,
+Left-align and normalize indels, check if REF alleles match the reference,
 split multiallelic sites into multiple rows; recover multiallelics from
-multiple rows.
+multiple rows. Left-alignment and normalization will only be applied if
+the *<<fasta_ref,--fasta-ref>>* option is supplied.
+
+*-c, --check-ref* 'e'|'w'|'x'|'s':: 
+    what to do when incorrect or missing REF allele is encountered: 
+    exit ('e'), warn ('w'), exclude ('x'), or set/fix ('s') bad sites.
+    The 'w' option can be combined with 'x' and 's'. Note that 's'
+    can swap alleles and will update genotypes (GT) and AC counts, 
+    but will not attempt to fix PL or other fields.
+
+*-d, --rm-dup* 'snps'|'indels'|'both'|'all'|'none'::
+    If a record is present in multiple files, output only the first instance,
+    see *--collapse* in *<<common_options,Common Options>>*.
+    Requires *-a, --allow-overlaps*.
 
 *-D, --remove-duplicates*::
-    remove duplicate lines of the same type
+    If a record is present in multiple files, output only the first instance.
+    Alias for *-d none*.  Requires *-a, --allow-overlaps*.
 
-*-f, --fasta-ref* 'FILE'::
-    reference sequence
+*-f, --fasta-ref* 'FILE'[[fasta_ref]]::
+    reference sequence. Supplying this option will turn on left-alignment
+    and normalization, however, see also the *<<do_not_normalize,--do-not-normalize>>*
+    option below.
 
 *-m, --multiallelics* <-|+>['snps'|'indels'|'both'|'any']::
     split multiallelic sites into biallelic records ('-') or join
@@ -1038,6 +1262,11 @@ multiple rows.
     'both'; if SNPs and indels should be merged into a single record, specify
     'any'.
 
+*-N, --do-not-normalize*[[do_not_normalize]]::
+    the '-c s' option can be used to fix or set the REF allele from the 
+    reference '-f'. The '-N' option will not turn on indel normalisation
+    as the '-f' option normally implies
+
 *-o, --output* 'FILE'::
     see *<<common_options,Common Options>>*
 
@@ -1059,13 +1288,16 @@ multiple rows.
 *-T, --targets-file* 'FILE'::
     see *<<common_options,Common Options>>*
 
+*--threads* 'INT'::
+    see *<<common_options,Common Options>>*
+
 *-w, --site-win* 'INT'::
     maximum distance between two records to consider when locally
     sorting variants which changed position during the realignment
 
 
 [[plugin]]
-=== bcftools plugin 'NAME' '[OPTIONS]' 'FILE' -- '[PLUGIN OPTIONS]'
+=== bcftools [plugin 'NAME'|+'NAME'] '[OPTIONS]' 'FILE' -- '[PLUGIN OPTIONS]'
 
 ==== VCF input options:
 
@@ -1097,20 +1329,34 @@ multiple rows.
 *-O, --output-type* 'b'|'u'|'z'|'v'::
     see *<<common_options,Common Options>>*
 
+*--threads* 'INT'::
+    see *<<common_options,Common Options>>*
+
 ==== Plugin options:
 
 *-h, --help*::
     list plugin's options
 
 *-l, --list-plugins*::
-    List all available plugins. If not installed systemwide, set the environment
-    variable LD_LIBRARY_PATH (linux) or DYLD_LIBRARY_PATH (Mac OS X) to include
-    directory where *libhts.so* is located.  The BCFTOOLS_PLUGINS
-    environment variable tells the program which directories to search.
+    List all available plugins.
++
+By default, appropriate system directories are searched for installed plugins.
+    You can override this by setting the BCFTOOLS_PLUGINS environment variable
+    to a colon-separated list of directories to search.
+    If BCFTOOLS_PLUGINS begins with a colon, ends with a colon, or contains
+    adjacent colons, the system directories are also searched at that position
+    in the list of directories.
++
+If htslib is not installed systemwide, set the environment variable
+    LD_LIBRARY_PATH (linux) or DYLD_LIBRARY_PATH (Mac OS X) to include the
+    directory where *libhts.so.1* is located.
 
 *-v, --verbose*::
     print debugging information to debug plugin failure
 
+*-V, --version*::
+    print version string and exit
+
 ==== List of plugins coming with the distribution:
 
 *counts*::
@@ -1147,9 +1393,13 @@ bcftools plugin
 # List available plugins
 bcftools plugin -l
 
-# One can run plugins in several ways
+# Run a plugin
 bcftools plugin counts in.vcf
+
+# Run a plugin using the abbreviated "+" notation
 bcftools +counts in.vcf
+
+# The input VCF can be streamed just like in other commands
 cat in.vcf | bcftools +counts
 
 # Print usage information of plugin "dosage"
@@ -1197,6 +1447,67 @@ void destroy(void);
 ----
 
 
+
+[[polysomy]]
+=== bcftools polysomy ['OPTIONS'] 'file.vcf.gz'
+Detect number of chromosomal copies in VCFs annotates with the Illumina's
+B-allele frequency (BAF) values. Note that this command is not compiled
+in by default, see the section *Optional Compilation with GSL* in the INSTALL 
+file for help.
+
+==== General options:
+
+*-o, --output-dir* 'path'::
+    output directory 
+
+*-r, --regions* 'chr'|'chr:pos'|'chr:from-to'|'chr:from-'[,...]::
+    see *<<common_options,Common Options>>*
+
+*-R, --regions-file* 'file'::
+    see *<<common_options,Common Options>>*
+
+*-s, --sample* 'string'::
+    samply name
+
+*-t, --targets* 'LIST'::
+    see *<<common_options,Common Options>>*
+
+*-T, --targets-file* 'FILE'::
+    see *<<common_options,Common Options>>*
+
+*-v, --verbose*::
+    verbose debugging output which gives hints about the thresholds and decisions made
+    by the program. Note that the exact output can change between versions.
+
+==== Algorithm options:
+
+*-b, --peak-size* 'float'::
+    the minimum peak size considered as a good match can be from the interval [0,1]
+    where larger is stricter
+
+*-c, --cn-penalty* 'float'::
+    a penalty for increasing copy number state. How this works: multiple peaks
+    are always a better fit than a single peak, therefore the program prefers 
+    a single peak (normal copy number) unless the absolute deviation of the
+    multiple peaks fit is significantly smaller. Here the meaning of
+    "significant" is given by the 'float' from the interval [0,1] where
+    larger is stricter.
+    
+*-f, --fit-th* 'float'::
+    threshold for goodness of fit (normalized absolute deviation), smaller is stricter
+
+*-i, --include-aa*::
+    include also the AA peak in CN2 and CN3 evaluation. This usually requires increasing *-f*.
+
+*-m, --min-fraction* 'float'::
+    minimum distinguishable fraction of aberrant cells. The experience shows that trustworthy
+    are estimates of 20% and more.
+
+*-p, --peak-symmetry* 'float'::
+    a heuristics to filter failed fits where the expected peak symmetry is violated.
+    The 'float' is from the interval [0,1] and larger is stricter
+
+
 [[query]]
 === bcftools query ['OPTIONS'] 'file.vcf.gz' ['file.vcf.gz' [...]]
 Extracts fields from VCF or BCF files and outputs them in user-defined format.
@@ -1242,6 +1553,10 @@ Extracts fields from VCF or BCF files and outputs them in user-defined format.
 *-T, --targets-file* 'file'::
     see *<<common_options,Common Options>>*
 
+*-u, --allow-undef-tags*::
+    do not throw an error if there are undefined tags in the format string,
+    print "." instead
+
 *-v, --vcf-list* 'FILE'::
     process multiple VCFs listed in the file
 
@@ -1302,20 +1617,22 @@ Emission probabilities:
 Transition probabilities:
   tAZ = P(AZ|HW)  .. from HW to AZ, the -a parameter
   tHW = P(HW|AZ)  .. from AZ to HW, the -H parameter
-  P(AZ|AZ) = 1 - P(HW|AZ) = 1 - tHW
-  P(HW|HW) = 1 - P(AZ|HW) = 1 - tAZ
 
   ci  = P_i(C)  .. probability of cross-over at site i, from genetic map
   AZi = P_i(AZ) .. probability of site i being AZ/non-AZ, scaled so that AZi+HWi = 1
   HWi = P_i(HW) 
 
-  P_{i+1}(AZ) = oAZ * max[(1-tHW) * (1-ci) * AZ{i-1} , tAZ * ci * (1-AZ{i-1})]
-  P_{i+1}(HW) = oHW * max[(1-tAZ) * (1-ci) * (1-AZ{i-1}) , tHW * ci * AZ{i-1}]
+  P_{i+1}(AZ) = oAZ * max[(1 - tAZ * ci) * AZ{i-1} , tAZ * ci * (1-AZ{i-1})]
+  P_{i+1}(HW) = oHW * max[(1 - tHW * ci) * (1-AZ{i-1}) , tHW * ci * AZ{i-1}]
 
 --------------------------------------
 
 ==== General Options:
 
+*--AF-dflt* 'FLOAT'::
+    in case allele frequency is not known, use the 'FLOAT'. By default, sites where
+    allele frequency cannot be determined, or is 0, are skipped.
+
 *--AF-tag* 'TAG'::
     use the specified INFO tag 'TAG' as an allele frequency estimate
     instead of the defaul AC and AN tags. Sites which do not have 'TAG'
@@ -1351,6 +1668,9 @@ Transition probabilities:
     be a single file or a file mask, where string "{CHROM}" is replaced with
     chromosome name.
 
+*-M, --rec-rate* 'FLOAT'::
+    constant recombination rate per bp
+
 *-r, --regions* 'chr'|'chr:pos'|'chr:from-to'|'chr:from-'[,...]::
     see *<<common_options,Common Options>>*
 
@@ -1388,7 +1708,7 @@ default only sites are compared, *-s*/*-S* must given to include also sample
 columns.
 
 *-1, --1st-allele-only*::
-    consider only 1st allele at multiallelic sites
+    consider only the 1st alternate allele at multiallelic sites
 
 *-c, --collapse* 'snps'|'indels'|'both'|'all'|'some'|'none'::
     see *<<common_options,Common Options>>*
@@ -1399,7 +1719,11 @@ columns.
 *--debug*::
     produce verbose per-site and per-sample output
 
-*-e, --exons* 'file.gz'::
+*-e, --exclude* 'EXPRESSION'::
+    exclude sites for which 'EXPRESSION' is true. For valid expressions see
+    *<<expressions,EXPRESSIONS>>*.
+
+*-E, --exons* 'file.gz'::
     tab-delimited file with exons for indel frameshifts statistics. The columns
     of the file are CHR, FROM, TO, with 1-based, inclusive, positions. The file
     is BGZF-compressed and indexed with tabix
@@ -1413,7 +1737,11 @@ columns.
 *-F, --fasta-ref* 'ref.fa'::
     faidx indexed reference sequence file to determine INDEL context
 
-*-i, --split-by-ID*::
+*-i, --include* 'EXPRESSION'::
+    include only sites for which 'EXPRESSION' is true. For valid expressions see
+    *<<expressions,EXPRESSIONS>>*.
+
+*-I, --split-by-ID*::
     collect stats separately for sites which have the ID column set ("known
     sites") or which do not have the ID column set ("novel sites").
 
@@ -1435,7 +1763,11 @@ columns.
 *-T, --targets-file* 'file'::
     see *<<common_options,Common Options>>*
 
+*-u, --user-tstv* '<TAG[:min:max:n]>'::
+    collect Ts/Tv stats for any tag using the given binning [0:1:100]
 
+*-v, --verbose*::
+    produce verbose per-site and per-sample output
 
 
 [[view]]
@@ -1476,11 +1808,17 @@ Convert between VCF and BCF. Former *bcftools subset*.
 *-T, --targets-file* 'file'::
     see *<<common_options,Common Options>>*
 
+*--threads* 'INT'::
+    see *<<common_options,Common Options>>*
+
 
 ==== Subset options:
 *-a, --trim-alt-alleles*::
     trim alternate alleles not seen in subset. Type A, G and R INFO and FORMAT fields will also be trimmed
 
+*--force-samples*::
+    only warn about unknown subset samples
+
 *-I, --no-update*::
     do not (re)calculate INFO fields for the subset (currently INFO/AC and INFO/AN)
 
@@ -1542,14 +1880,14 @@ Convert between VCF and BCF. Former *bcftools subset*.
 *-P, --exclude-phased*::
     exclude sites where all samples are phased
 
-*-q, --min-af* 'FLOAT'[':nref'|':alt1'|':minor'|:'major'|:'nonmajor']::
+*-q, --min-af* 'FLOAT'[':nref'|':alt1'|':minor'|':major'|':nonmajor']::
     minimum allele frequency (INFO/AC / INFO/AN) of sites to be printed.
     Specifying the type of allele is optional and can be set to 
     non-reference ('nref', the default), 1st alternate  ('alt1'), the least 
     frequent ('minor'), the most frequent ('major') or sum of all but the 
     most frequent ('nonmajor') alleles.
 
-*-Q, --max-af* 'FLOAT'[':nref'|':alt1'|':minor'|:'major'|:'nonmajor']::
+*-Q, --max-af* 'FLOAT'[':nref'|':alt1'|':minor'|':major'|':nonmajor']::
     maximum allele frequency (INFO/AC / INFO/AN) of sites to be printed.
     Specifying the type of allele is optional and can be set to 
     non-reference ('nref', the default), 1st alternate  ('alt1'), the least 
@@ -1563,17 +1901,37 @@ Convert between VCF and BCF. Former *bcftools subset*.
     exclude sites without a called genotype
 
 *-v, --types* 'snps'|'indels'|'mnps'|'other'::
-    comma-separated list of variant types to select
+    comma-separated list of variant types to select. Site is selected if 
+    any of the ALT alleles is of the type requested. Types are determined 
+    by comparing the REF and ALT alleles in the VCF record not INFO tags 
+    like INFO/INDEL or INFO/VT. Use *--include* to select based on INFO 
+    tags.
 
 *-V, --exclude-types* 'snps'|'indels'|'mnps'|'other'::
-    comma-separated list of variant types to exclude
+    comma-separated list of variant types to exclude. Site is excluded if 
+    any of the ALT alleles is of the type requested. Types are determined 
+    by comparing the REF and ALT alleles in the VCF record not INFO tags 
+    like INFO/INDEL or INFO/VT. Use *--exclude* to exclude based on INFO tags.
 
 *-x, --private*::
-    print sites where only the subset samples carry an non-reference allele
+    print sites where only the subset samples carry an non-reference allele.
+    Requires *--samples* or *--samples-file*.
 
 *-X, --exclude-private*::
     exclude sites where only the subset samples carry an non-reference allele
 
+[[help]]
+=== bcftools help ['COMMAND'] | bcftools --help ['COMMAND']
+Display  a  brief usage message listing the bcftools commands available.  If the name of a command is also given, e.g., bcftools help view, the detailed usage message for that particular command is displayed.
+
+[[version]]
+=== bcftools ['--version'|'-v']
+Display the version numbers and copyright information for bcftools and the important libraries used by bcftools.
+
+[[version-only]]
+=== bcftools ['--version-only']
+Display the full bcftools version number in a machine-readable format.
+
 
 [[expressions]]
 EXPRESSIONS
@@ -1615,12 +1973,21 @@ These filtering expressions are accepted by *<<annotate,annotate>>*,
 
         INFO/DP or DP
         FORMAT/DV, FMT/DV, or DV
-        FILTER, QUAL, ID, REF, ALT[0]
+        FILTER, QUAL, ID, POS, REF, ALT[0]
 
 * 1 (or 0) to test the presence (or absence) of a flag
 
         FlagA=1 && FlagB=0
 
+* "." to test missing values
+
+        DP=".", DP!=".", ALT="."
+
+* missing genotypes can be matched regardless of phase and ploidy (".|.", "./.", ".")
+using this expression
+
+        GT="."
+
 * TYPE for variant type in REF,ALT columns (indel,snp,mnp,ref,other)
 
         TYPE="indel" | TYPE="snp"
@@ -1663,6 +2030,10 @@ not "dp" instead of "DP".
 
     MIN(DP)>10 & MIN(DV)>3
 
+    FMT/DP>10  & FMT/GQ>10 .. both conditions must be satisfied within one sample
+
+    FMT/DP>10 && FMT/GQ>10 .. the conditions can be satisfied in different samples
+
     QUAL>10 |  FMT/GQ>10   .. selects only GQ>10 samples
 
     QUAL>10 || FMT/GQ>10   .. selects all samples at QUAL>10 sites
@@ -1677,6 +2048,8 @@ not "dp" instead of "DP".
 
     MAF[0]<0.05    .. select rare variants at 5% cutoff
 
+    POS>=100   .. restrict your range query, e.g. 20:100-200 to strictly sites with POS in that range.
+
 --
 
 *Shell expansion:*
diff --git a/filter.c b/filter.c
index aca8835..c56ae6d 100644
--- a/filter.c
+++ b/filter.c
@@ -1,6 +1,6 @@
 /*  filter.c -- filter expressions.
 
-    Copyright (C) 2013-2014 Genome Research Ltd.
+    Copyright (C) 2013-2015 Genome Research Ltd.
 
     Author: Petr Danecek <pd3 at sanger.ac.uk>
 
@@ -41,7 +41,7 @@ typedef struct _token_t
     char *key;          // set only for string constants, otherwise NULL
     char *tag;          // for debugging and printout only, VCF tag name
     float threshold;    // filtering threshold
-    int hdr_id;         // BCF header lookup ID
+    int hdr_id, type;   // BCF header lookup ID and one of BCF_HT_* types
     int idx;            // 0-based index to VCF vectors, -1: not a vector, -2: any field ([*])
     void (*setter)(filter_t *, bcf1_t *, struct _token_t *);
     int (*comparator)(struct _token_t *, struct _token_t *, int op_type, bcf1_t *);
@@ -51,7 +51,7 @@ typedef struct _token_t
     // modified on filter evaluation at each VCF line
     float *values;      // In case str_value is set, values[0] is one sample's string length
     char *str_value;    //  and values[0]*nsamples gives the total length;
-    int is_str;
+    int is_str, is_missing; // is_missing is set only for constants, variables are controled via nvalues
     int pass_site;          // -1 not applicable, 0 fails, >0 pass
     uint8_t *pass_samples;  // status of individual samples
     int nsamples;           // number of samples
@@ -251,15 +251,25 @@ static void filters_set_info(filter_t *flt, bcf1_t *line, token_t *tok)
     }
     else if ( line->d.info[i].type==BCF_BT_FLOAT )
     {
-        tok->values[0] = line->d.info[i].v1.f;
+        if ( bcf_float_is_missing(line->d.info[i].v1.f) ) tok->nvalues = 0;
+        else
+        {
+            tok->values[0] = line->d.info[i].v1.f;
+            tok->nvalues   = 1;
+        }
         tok->str_value = NULL;
-        tok->nvalues   = 1;
     }
     else
     {
-        tok->values[0] = line->d.info[i].v1.i;
+        if ( line->d.info[i].type==BCF_BT_INT8 && line->d.info[i].v1.i==bcf_int8_missing ) tok->nvalues = 0;
+        else if ( line->d.info[i].type==BCF_BT_INT16 && line->d.info[i].v1.i==bcf_int16_missing ) tok->nvalues = 0;
+        else if ( line->d.info[i].type==BCF_BT_INT32 && line->d.info[i].v1.i==bcf_int32_missing ) tok->nvalues = 0;
+        else
+        {
+            tok->values[0] = line->d.info[i].v1.i;
+            tok->nvalues   = 1;
+        }
         tok->str_value = NULL;
-        tok->nvalues   = 1;
     }
 }
 static int filters_cmp_filter(token_t *atok, token_t *btok, int op_type, bcf1_t *line)
@@ -354,6 +364,12 @@ static int bcf_get_info_value(bcf1_t *line, int info_id, int ivec, void *value)
     return -1;  // this shouldn't happen
 }
 
+static void filters_set_pos(filter_t *flt, bcf1_t *line, token_t *tok)
+{
+    tok->values[0] = line->pos+1;
+    tok->nvalues = 1;
+}
+
 static void filters_set_info_int(filter_t *flt, bcf1_t *line, token_t *tok)
 {
     if ( tok->idx==-2 )
@@ -490,6 +506,7 @@ static void filters_set_format_float(filter_t *flt, bcf1_t *line, token_t *tok)
             tok->nsamples = tok->nvalues = nsmpl;
         }
     }
+    tok->nsamples = tok->nvalues;
 }
 static void filters_set_format_string(filter_t *flt, bcf1_t *line, token_t *tok)
 {
@@ -551,12 +568,39 @@ static void filters_set_genotype_string(filter_t *flt, bcf1_t *line, token_t *to
         return;
     }
     int i, blen = 3, nsmpl = bcf_hdr_nsamples(flt->hdr);
-    kstring_t str; str.s = tok->str_value; str.m = tok->values[0] * nsmpl; str.l = 0;
+    kstring_t str;
+
+gt_length_too_big:
+    str.s = tok->str_value; str.m = tok->values[0] * nsmpl; str.l = 0;
     for (i=0; i<nsmpl; i++)
     {
         int plen = str.l;
-        bcf_format_gt(fmt, i, &str);
-        assert( str.l - plen <= blen ); // increase blen if this fails
+
+        #define BRANCH(type_t) { \
+            type_t *ptr = (type_t*) (fmt->p + i*fmt->size); \
+            if ( !(ptr[0]>>1) ) kputc('.',&str); \
+        }
+        switch (fmt->type) {
+            case BCF_BT_INT8:  BRANCH(int8_t); break;
+            case BCF_BT_INT16: BRANCH(int16_t); break;
+            case BCF_BT_INT32: BRANCH(int32_t); break;
+            default: fprintf(stderr,"FIXME: type %d in bcf_format_gt?\n", fmt->type); abort(); break;
+        }
+        #undef BRANCH
+
+        if ( plen==str.l )
+        {
+            bcf_format_gt(fmt, i, &str);
+            if ( str.l - plen > blen )
+            {
+                // too many alternate alleles or ploidy is too large, the genotype does not fit
+                // three characters ("0/0" vs "10/10").
+                tok->str_value = str.s;
+                blen *= 2;
+                goto gt_length_too_big;
+            }
+        }
+
         plen = str.l - plen;
         while ( plen<blen )
         {
@@ -587,7 +631,7 @@ static void filters_set_alt_string(filter_t *flt, bcf1_t *line, token_t *tok)
         else
             kputc('.', &str);
     }
-    else
+    else if ( line->n_allele>1 )
     {
         kputs(line->d.allele[1], &str);
         int i;
@@ -597,6 +641,8 @@ static void filters_set_alt_string(filter_t *flt, bcf1_t *line, token_t *tok)
             kputs(line->d.allele[i], &str);
         }
     }
+    else if ( line->n_allele==1 )
+        kputc('.', &str);
     tok->nvalues = str.l;
     tok->values[0] = str.m;
     tok->str_value = str.s;
@@ -625,7 +671,12 @@ static void filters_set_ac(filter_t *flt, bcf1_t *line, token_t *tok)
     if ( tok->idx>=0 )
     {
         tok->nvalues = 1;
-        tok->values[0] = flt->tmpi[tok->idx+1];
+        tok->values[0] = tok->idx+1<line->n_allele ? flt->tmpi[tok->idx+1] : 0;
+    }
+    else if ( line->n_allele==1 )   // no ALT
+    {
+        tok->nvalues = 1;
+        tok->values[0] = 0;
     }
     else
     {
@@ -800,7 +851,7 @@ static void set_strlen(filter_t *flt, bcf1_t *line, token_t *tok)
     if ( !has_values ) { (atok)->nvalues = 0; (atok)->nsamples = 0; } \
 }
 
-static int vector_logic_and(token_t *atok, token_t *btok)
+static int vector_logic_and(token_t *atok, token_t *btok, int and_type)
 {
     // We are comparing either two scalars (result of INFO tag vs a threshold), two vectors (two FORMAT fields),
     // or a vector and a scalar (FORMAT field vs threshold)
@@ -813,10 +864,29 @@ static int vector_logic_and(token_t *atok, token_t *btok)
     if ( !atok->nsamples && !btok->nsamples ) return atok->pass_site && btok->pass_site;
     if ( atok->nsamples && btok->nsamples )
     {
-        for (i=0; i<atok->nsamples; i++)
+        if ( and_type==TOK_AND )
         {
-            atok->pass_samples[i] = atok->pass_samples[i] && btok->pass_samples[i];
-            if ( !pass_site && atok->pass_samples[i] ) pass_site = 1;
+            // perform AND within a sample
+            for (i=0; i<atok->nsamples; i++)
+            {
+                atok->pass_samples[i] = atok->pass_samples[i] && btok->pass_samples[i];
+                if ( !pass_site && atok->pass_samples[i] ) pass_site = 1;
+            }
+        }
+        else
+        {
+            // perform AND across samples
+            int pass_a = 0, pass_b = 0;
+            for (i=0; i<atok->nsamples; i++)
+            {
+                if ( atok->pass_samples[i] ) pass_a = 1;
+                atok->pass_samples[i] = atok->pass_samples[i] && btok->pass_samples[i];
+            }
+            for (i=0; i<btok->nsamples; i++)
+            {
+                if ( btok->pass_samples[i] ) { pass_b = 1; break; }
+            }
+            pass_site = pass_a && pass_b;
         }
         return pass_site;
     }
@@ -903,6 +973,13 @@ static int vector_logic_or(token_t *atok, token_t *btok, int or_type)
     return pass_site;
 }
 
+#define CMP_MISSING(atok,btok,CMP_OP,ret) \
+{ \
+    if ( (atok)->nsamples || (btok)->nsamples ) error("todo: Querying of missing values in FORMAT\n"); \
+    token_t *tok = (atok)->is_missing ? (btok) : (atok); \
+    (ret) = ( tok->nvalues CMP_OP 1 ) ? 0 : 1; \
+}
+
 #define CMP_VECTORS(atok,btok,CMP_OP,ret) \
 { \
     int i, j, has_values = 0, pass_site = 0; \
@@ -964,11 +1041,7 @@ static int vector_logic_or(token_t *atok, token_t *btok, int or_type)
         } \
         else \
         { \
-            if ( bcf_float_is_missing((atok)->values[0]) || bcf_float_is_missing((btok)->values[0]) ) \
-            { \
-                (atok)->nvalues = 0; (atok)->nsamples = 0; (ret) = 0; \
-            } \
-            else if ( (atok)->values[0] CMP_OP (btok)->values[0] ) { pass_site = 1; } \
+            if ( (atok)->values[0] CMP_OP (btok)->values[0] ) { pass_site = 1; } \
         } \
         /*fprintf(stderr,"pass=%d\n", pass_site);*/ \
         (ret) = pass_site; \
@@ -1076,6 +1149,7 @@ static int filters_init1(filter_t *filter, char *str, int len, token_t *tok)
         tok->key[len-2] = 0;
         tok->is_str = 1;
         tok->nvalues = len-2;
+        if ( !strcmp(".",tok->key) ) tok->is_missing = 1;
         return 0;
     }
 
@@ -1138,6 +1212,12 @@ static int filters_init1(filter_t *filter, char *str, int len, token_t *tok)
             tok->tag = strdup("ID");
             return 0;
         }
+        else if ( !strncasecmp(str,"POS",len) )
+        {
+            tok->setter = &filters_set_pos;
+            tok->tag = strdup("POS");
+            return 0;
+        }
         else if ( !strncasecmp(str,"REF",len) )
         {
             tok->setter = &filters_set_ref_string;
@@ -1197,6 +1277,7 @@ static int filters_init1(filter_t *filter, char *str, int len, token_t *tok)
         }
         if ( is_fmt==-1 ) is_fmt = 0;
     }
+    tok->type = is_fmt ? BCF_HL_FMT : BCF_HL_INFO;
     if ( is_fmt ) filter->max_unpack |= BCF_UN_FMT;
     if ( tok->hdr_id>=0 )
     {
@@ -1228,25 +1309,25 @@ static int filters_init1(filter_t *filter, char *str, int len, token_t *tok)
             {
                 if ( bcf_hdr_id2type(filter->hdr,BCF_HL_INFO,tok->hdr_id) == BCF_HT_STR ) tok->is_str = 1;
                 if ( bcf_hdr_id2number(filter->hdr,BCF_HL_INFO,tok->hdr_id)==1 )
-                tok->setter = filters_set_info;
-            else
-            {
-                switch ( bcf_hdr_id2type(filter->hdr,BCF_HL_INFO,tok->hdr_id) )
+                    tok->setter = filters_set_info;
+                else
                 {
-                    case BCF_HT_INT:  tok->setter = &filters_set_info_int; break;
-                    case BCF_HT_REAL: tok->setter = &filters_set_info_float; break;
-                    case BCF_HT_STR:  tok->setter = &filters_set_info_string; tok->is_str = 1; break;
-                    default: error("[%s:%d %s] FIXME\n", __FILE__,__LINE__,__FUNCTION__);
+                    switch ( bcf_hdr_id2type(filter->hdr,BCF_HL_INFO,tok->hdr_id) )
+                    {
+                        case BCF_HT_INT:  tok->setter = &filters_set_info_int; break;
+                        case BCF_HT_REAL: tok->setter = &filters_set_info_float; break;
+                        case BCF_HT_STR:  tok->setter = &filters_set_info_string; tok->is_str = 1; break;
+                        default: error("[%s:%d %s] FIXME\n", __FILE__,__LINE__,__FUNCTION__);
+                    }
+                    if(!is_array) tok->idx = -2;
                 }
-                    //tok->idx = -2;
-            }
             }
             filter->max_unpack |= BCF_UN_INFO;
-            }
-            tok->tag = strdup(tmp.s);
-            if ( tmp.s ) free(tmp.s);
-            return 0;
         }
+        tok->tag = strdup(tmp.s);
+        if ( tmp.s ) free(tmp.s);
+        return 0;
+    }
     else if ( !strcasecmp(tmp.s,"ALT") )
     {
         tok->setter = &filters_set_alt_string;
@@ -1420,10 +1501,23 @@ filter_t *filter_init(bcf_hdr_t *hdr, const char *str)
     // list of operators and convert the strings (e.g. "PASS") to BCF ids. The string value token must be
     // just before or after the FILTER token and they must be followed with a comparison operator.
     // At this point we also initialize regex expressions which, in RPN, must preceed the LIKE/NLIKE operator.
+    // Additionally, treat "." as missing value rather than a string in numeric equalities.
     // This code is fragile: improve me.
     int i;
     for (i=0; i<nout; i++)
     {
+        if ( out[i].tok_type==TOK_EQ || out[i].tok_type==TOK_NE )
+        {
+            // Look for j="." and k numeric type
+            int j = i-1, k = i-2;
+            if ( !out[j].is_str ) { k = i-1, j = i-2; }
+            if ( out[k].hdr_id>0 && out[j].is_str && !strcmp(".",out[j].key) )
+            {
+                int type = bcf_hdr_id2type(filter->hdr,out[k].type,out[k].hdr_id);
+                if ( type==BCF_HT_INT ) { out[j].is_str = 0; out[j].is_missing = 1; bcf_float_set_missing(out[j].values[0]); }
+                if ( type==BCF_HT_REAL ) { out[j].is_str = 0; out[j].is_missing = 1; bcf_float_set_missing(out[j].values[0]); }
+            }
+        }
         if ( out[i].tok_type==TOK_LIKE || out[i].tok_type==TOK_NLIKE )
         {
             int j = i-1;
@@ -1455,7 +1549,11 @@ filter_t *filter_init(bcf_hdr_t *hdr, const char *str)
         {
             if ( i+1==nout ) error("Could not parse the expression: %s\n", filter->str);
             int j = i+1;
-            if ( out[j].tok_type==TOK_EQ || out[j].tok_type==TOK_NE || out[j].tok_type==TOK_LIKE ) j = i - 1;
+            if ( out[j].tok_type==TOK_EQ || out[j].tok_type==TOK_NE ) j = i - 1;    // the expression has "value"=FILTER rather than FILTER="value"
+            if ( out[j].tok_type==TOK_LIKE ) out[j].tok_type = TOK_EQ;              // for FILTER, ~ and !~ work the same way as = and !=
+            if ( out[j].tok_type==TOK_NLIKE ) out[j].tok_type = TOK_NE;
+            if ( out[j+1].tok_type==TOK_LIKE ) out[j+1].tok_type = TOK_EQ;
+            if ( out[j+1].tok_type==TOK_NLIKE ) out[j+1].tok_type = TOK_NE;
             if ( out[j].tok_type!=TOK_VAL || !out[j].key )
                 error("[%s:%d %s] Could not parse the expression, an unquoted string value perhaps? %s\n", __FILE__,__LINE__,__FUNCTION__, filter->str);
             if ( strcmp(".",out[j].key) )
@@ -1575,7 +1673,7 @@ int filter_test(filter_t *filter, bcf1_t *line, const uint8_t **samples)
         {
             if ( filter->flt_stack[nstack-1]->pass_site<0 || filter->flt_stack[nstack-2]->pass_site<0 )
                 error("Error occurred while processing the filter \"%s\" (%d %d AND)\n", filter->str,filter->flt_stack[nstack-2]->pass_site,filter->flt_stack[nstack-1]->pass_site);
-            filter->flt_stack[nstack-2]->pass_site = vector_logic_and(filter->flt_stack[nstack-2],filter->flt_stack[nstack-1]);
+            filter->flt_stack[nstack-2]->pass_site = vector_logic_and(filter->flt_stack[nstack-2],filter->flt_stack[nstack-1], filter->filters[i].tok_type);
             nstack--;
             continue;
         }
@@ -1608,7 +1706,16 @@ int filter_test(filter_t *filter, bcf1_t *line, const uint8_t **samples)
         int is_true = 0;
         if ( !filter->flt_stack[nstack-1]->nvalues || !filter->flt_stack[nstack-2]->nvalues )
         {
-            filter->flt_stack[nstack-2]->nvalues = filter->flt_stack[nstack-2]->nsamples = 0;
+            int skip = 0;
+            if ( !filter->flt_stack[nstack-2]->is_missing && !filter->flt_stack[nstack-1]->is_missing ) skip = 1;
+            if ( filter->filters[i].tok_type != TOK_EQ  && filter->filters[i].tok_type != TOK_NE ) skip = 1;
+
+            if ( skip ) 
+                filter->flt_stack[nstack-2]->nvalues = filter->flt_stack[nstack-2]->nsamples = 0;
+            else if ( filter->filters[i].tok_type == TOK_EQ )
+                CMP_MISSING(filter->flt_stack[nstack-2],filter->flt_stack[nstack-1],==,is_true)
+            else if ( filter->filters[i].tok_type == TOK_NE )
+                CMP_MISSING(filter->flt_stack[nstack-2],filter->flt_stack[nstack-1],!=,is_true)
         }
         else if ( filter->filters[i].tok_type == TOK_EQ )
         {
@@ -1675,3 +1782,7 @@ int filter_test(filter_t *filter, bcf1_t *line, const uint8_t **samples)
     return filter->flt_stack[0]->pass_site;
 }
 
+int filter_max_unpack(filter_t *flt)
+{
+    return flt->max_unpack;
+}
diff --git a/filter.h b/filter.h
index 132ef31..ccd3fe3 100644
--- a/filter.h
+++ b/filter.h
@@ -47,5 +47,6 @@ void filter_destroy(filter_t *filter);
 int filter_test(filter_t *filter, bcf1_t *rec, const uint8_t **samples);
 
 void filter_expression_info(FILE *fp);
+int filter_max_unpack(filter_t *filter);
 
 #endif
diff --git a/gvcf.c b/gvcf.c
index bba5df7..b82d658 100644
--- a/gvcf.c
+++ b/gvcf.c
@@ -1,6 +1,6 @@
 /*  gvcf.c -- support for gVCF files.
 
-    Copyright (C) 2014 Genome Research Ltd.
+    Copyright (C) 2014-2015 Genome Research Ltd.
 
     Author: Petr Danecek <pd3 at sanger.ac.uk>
 
@@ -22,33 +22,117 @@ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
 FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
 DEALINGS IN THE SOFTWARE.  */
 
-#include "call.h"
+#include "gvcf.h"
+#include "bcftools.h"
 
-void gvcf_write(htsFile *fh, gvcf_t *gvcf, bcf_hdr_t *hdr, bcf1_t *rec, int is_ref)
+struct _gvcf_t
+{
+    int *dp_range, ndp_range;   // per-sample DP ranges
+    int prev_range;             // 0 if not in a block
+    int32_t *dp, mdp, *pl, mpl, npl;
+    int32_t *tmp, mtmp, *gts, ngts,mgts, nqsum,mqsum;
+    float *qsum;
+    int32_t rid, start, end, min_dp;
+    kstring_t als;
+    bcf1_t *line;
+};
+
+void gvcf_update_header(gvcf_t *gvcf, bcf_hdr_t *hdr)
+{
+    bcf_hdr_append(hdr,"##INFO=<ID=END,Number=1,Type=Integer,Description=\"End position of the variant described in this record\">");
+    bcf_hdr_append(hdr,"##INFO=<ID=MinDP,Number=1,Type=Integer,Description=\"Minimum per-sample depth in this gVCF block\">");
+}
+
+gvcf_t *gvcf_init(const char *dp_ranges)
+{
+    gvcf_t *gvcf = (gvcf_t*) calloc(1,sizeof(gvcf_t));
+    gvcf->line = bcf_init();
+
+    int n = 1;
+    const char *ss = dp_ranges;
+    while ( *ss )
+    {
+        if ( *ss==',' ) n++;
+        ss++;
+    }
+    gvcf->ndp_range = n;
+    gvcf->dp_range  = (int*) malloc(sizeof(int)*gvcf->ndp_range);
+
+    n  = 0;
+    ss = dp_ranges;
+    while ( *ss )
+    {
+        char *se = (char*) ss;
+        gvcf->dp_range[n++] = strtol(ss,&se,10);
+        if ( se==ss ) return NULL;
+        if ( *se==',' && se[1] ) { ss = se+1; continue; }
+        else if ( !*se ) break;
+        return NULL;
+    }
+    return gvcf;
+}
+
+void gvcf_destroy(gvcf_t *gvcf)
+{
+    free(gvcf->dp_range);
+    free(gvcf->dp);
+    free(gvcf->pl);
+    free(gvcf->tmp);
+    free(gvcf->qsum);
+    free(gvcf->gts);
+    free(gvcf->als.s);
+    if ( gvcf->line ) bcf_destroy(gvcf->line);
+    free(gvcf);
+}
+
+bcf1_t *gvcf_write(gvcf_t *gvcf, htsFile *fh, bcf_hdr_t *hdr, bcf1_t *rec, int is_ref)
 {
     int i, ret, nsmpl = bcf_hdr_nsamples(hdr);
+    int can_collapse = is_ref ? 1 : 0;
+    int32_t dp_range = 0, min_dp = 0;
+
+    // No record and nothing to flush?
+    if ( !rec && !gvcf->prev_range ) return NULL;
 
-    // Flush gVCF block if chr changed, non-ref call encountered, depth is too
-    // low, or no more records to come
-    if ( rec && is_ref )
+    // Flush gVCF block if there are no more records, chr changed, a gap
+    // encountered, or other conditions not met (block broken by a non-ref or DP too low).
+    int needs_flush = can_collapse ? 0 : 1;
+
+
+    // Can the record be included in a gVCF block? That is, is this a ref-only site?
+    if ( rec && can_collapse )
     {
         bcf_unpack(rec, BCF_UN_ALL);
 
         // per-sample depth
-        ret = bcf_get_format_int32(hdr, rec, "DP", &gvcf->dp, &gvcf->mdp);
+        ret = bcf_get_format_int32(hdr, rec, "DP", &gvcf->tmp, &gvcf->mtmp);
         if ( ret==nsmpl )
         {
-            for (i=0; i<nsmpl; i++)
-                if ( gvcf->dp[i] < gvcf->min_dp ) break;
-            if ( i<nsmpl )
+            min_dp = gvcf->tmp[0];
+            for (i=1; i<nsmpl; i++)
+                if ( min_dp > gvcf->tmp[i] ) min_dp = gvcf->tmp[i];
+
+            for (i=0; i<gvcf->ndp_range; i++)
+                if ( min_dp < gvcf->dp_range[i] ) break;
+
+            dp_range = i;
+            if ( !dp_range )
             {
-                is_ref = 0;  // the depth is too low
-                rec = NULL;
+                // leave the record unchanged, DP is too small. Alternatively, return NULL here
+                // to skip these sites
+                needs_flush  = 1;
+                can_collapse = 0;
             }
         }
+        else
+            needs_flush = 1;       // DP field not present
     }
 
-    if ( gvcf->rid!=-1 && (!rec || gvcf->rid!=rec->rid || !is_ref || rec->pos > gvcf->end+1) )
+    if ( gvcf->prev_range && gvcf->prev_range!=dp_range ) needs_flush = 1;
+    if ( !rec || gvcf->rid!=rec->rid || rec->pos > gvcf->end+1 ) needs_flush = 1;
+
+    // If prev_range is set, something can be flushed
+    if ( gvcf->prev_range && needs_flush )
     {
         // mpileup can output two records with the same position, SNP and
         // indel. Make sure the end position does not include the non-variant
@@ -61,29 +145,83 @@ void gvcf_write(htsFile *fh, gvcf_t *gvcf, bcf_hdr_t *hdr, bcf1_t *rec, int is_r
         gvcf->line->rid  = gvcf->rid;
         gvcf->line->pos  = gvcf->start;
         gvcf->line->rlen = gvcf->end - gvcf->start;
-        bcf_update_alleles_str(hdr, gvcf->line, gvcf->ref);
-        bcf_update_info_int32(hdr, gvcf->line, "END", &gvcf->end, 1);
-        bcf_update_genotypes(hdr, gvcf->line, gvcf->gt, nsmpl*2);
+        bcf_update_alleles_str(hdr, gvcf->line, gvcf->als.s);
+        if ( gvcf->start+1 < gvcf->end )    // create gVCF record only if it spans at least two sites
+            bcf_update_info_int32(hdr, gvcf->line, "END", &gvcf->end, 1);
+        bcf_update_info_int32(hdr, gvcf->line, "MinDP", &gvcf->min_dp, 1);
+        if ( gvcf->nqsum>0 )
+            bcf_update_info_float(hdr, gvcf->line, "QS", gvcf->qsum, gvcf->nqsum);
+        if ( gvcf->ngts )
+            bcf_update_genotypes(hdr,gvcf->line,gvcf->gts,gvcf->ngts);
+        if ( gvcf->npl>0 )
+            bcf_update_format_int32(hdr, gvcf->line, "PL", gvcf->pl, gvcf->npl);
+        bcf_update_format_int32(hdr, gvcf->line, "DP", gvcf->dp, nsmpl);
         bcf_write1(fh, hdr, gvcf->line);
+        gvcf->prev_range = 0;
+        gvcf->rid  = -1;
+        gvcf->npl  = 0;
+        gvcf->nqsum = 0;
+        gvcf->ngts  = 0;
 
-        gvcf->rid = -1;
+        if ( !rec ) return NULL;     // just flushing the buffer, this was last record
     }
 
-    if ( !rec ) return;
-
-    if ( is_ref )
+    if ( can_collapse )
     {
-        if ( gvcf->rid==-1 )
+        if ( !gvcf->prev_range )
         {
+            hts_expand(int32_t,nsmpl,gvcf->mdp,gvcf->dp);
+            memcpy(gvcf->dp,gvcf->tmp,nsmpl*sizeof(int32_t));   // tmp still contains DP from rec
+            gvcf->npl = bcf_get_format_int32(hdr, rec, "PL", &gvcf->pl, &gvcf->mpl);
+
+            gvcf->nqsum = bcf_get_info_float(hdr,rec,"QS",&gvcf->qsum,&gvcf->mqsum);
+            gvcf->ngts  = bcf_get_genotypes(hdr,rec,&gvcf->gts,&gvcf->mgts);
+
             gvcf->rid    = rec->rid;
             gvcf->start  = rec->pos;
-            gvcf->ref[0] = rec->d.allele[0][0];
-            gvcf->ref[1] = 0;
+            gvcf->als.l = 0;
+            kputs(rec->d.allele[0],&gvcf->als);
+            for (i=1; i<rec->n_allele; i++)
+            {
+                kputc(',',&gvcf->als);
+                kputs(rec->d.allele[i],&gvcf->als);
+            }
+            gvcf->min_dp = min_dp;
+        }
+        else
+        {
+            if ( gvcf->min_dp > min_dp ) gvcf->min_dp = min_dp;
+            for (i=0; i<nsmpl; i++)
+                if ( gvcf->dp[i] > gvcf->tmp[i] ) gvcf->dp[i] = gvcf->tmp[i];
+            ret = bcf_get_format_int32(hdr, rec, "PL", &gvcf->tmp, &gvcf->mtmp);
+            if ( ret>=0 )
+            {
+                if ( ret!=nsmpl*3 ) error("Unexpected number of PL fields\n");
+                for (i=0; i<nsmpl; i++)
+                {
+                    if ( gvcf->pl[3*i+1] > gvcf->tmp[3*i+1] )
+                    {
+                        gvcf->pl[3*i+1] = gvcf->tmp[3*i+1];
+                        gvcf->pl[3*i+2] = gvcf->tmp[3*i+2];
+                    }
+                    else if ( gvcf->pl[3*i+1]==gvcf->tmp[3*i+1] && gvcf->pl[3*i+2] > gvcf->tmp[3*i+2] )
+                        gvcf->pl[3*i+2] = gvcf->tmp[3*i+2];
+                }
+            }
+            else
+                gvcf->npl = 0;
         }
-        gvcf->end = rec->pos;
-        return;
+        gvcf->prev_range = dp_range;
+        if ( bcf_get_info_int32(hdr,rec,"END",&gvcf->tmp,&gvcf->mtmp)==1 )
+            gvcf->end = gvcf->tmp[0] - 1;   // from 1-based to 0-based
+        else
+            gvcf->end = rec->pos;
+        return NULL;
     }
 
-    bcf_write1(fh, hdr, rec);
+    if ( is_ref && min_dp )
+        bcf_update_info_int32(hdr, rec, "MinDP", &min_dp, 1);
+
+    return rec;
 }
 
diff --git a/gvcf.h b/gvcf.h
new file mode 100644
index 0000000..784e1f6
--- /dev/null
+++ b/gvcf.h
@@ -0,0 +1,41 @@
+/* gvcf.[ch] - Helper functions for gVCF support
+
+   The MIT License
+
+   Copyright (c) 2015 Genome Research Ltd.
+
+   Author: Petr Danecek <pd3 at sanger.ac.uk>
+   
+   Permission is hereby granted, free of charge, to any person obtaining a copy
+   of this software and associated documentation files (the "Software"), to deal
+   in the Software without restriction, including without limitation the rights
+   to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+   copies of the Software, and to permit persons to whom the Software is
+   furnished to do so, subject to the following conditions:
+   
+   The above copyright notice and this permission notice shall be included in
+   all copies or substantial portions of the Software.
+   
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+   IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+   FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+   AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+   LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+   OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+   THE SOFTWARE.
+
+ */
+
+#ifndef __GVCF_H__
+#define __GVCF_H__
+
+#include "bcftools.h"
+
+typedef struct _gvcf_t gvcf_t;
+
+gvcf_t *gvcf_init(const char *dp_ranges);
+void gvcf_update_header(gvcf_t *gvcf, bcf_hdr_t *hdr);
+bcf1_t *gvcf_write(gvcf_t *gvcf, htsFile *fh, bcf_hdr_t *hdr, bcf1_t *rec, int is_ref);
+void gvcf_destroy(gvcf_t *gvcf);
+
+#endif
diff --git a/main.c b/main.c
index 98d8ee1..f08b5c7 100644
--- a/main.c
+++ b/main.c
@@ -138,7 +138,7 @@ static cmd_t cmds[] =
     },
     { .func  = main_vcfcnv,
       .alias = "cnv",
-      .help  = "-HMM CNV calling"    // do not advertise yet
+      .help  = "HMM CNV calling"
     },
     { .func  = main_vcffilter,
       .alias = "filter",
@@ -151,7 +151,7 @@ static cmd_t cmds[] =
 #if USE_GPL
     { .func  = main_polysomy,
       .alias = "polysomy",
-      .help  = "-detect number of chromosomal copies",
+      .help  = "detect number of chromosomal copies",
     },
 #endif
     { .func  = main_vcfroh,
@@ -188,7 +188,7 @@ static void usage(FILE *fp)
 #endif
     fprintf(fp, "Version: %s (using htslib %s)\n", bcftools_version(), hts_version());
     fprintf(fp, "\n");
-    fprintf(fp, "Usage:   bcftools <command> <argument>\n");
+    fprintf(fp, "Usage:   bcftools [--version|--version-only] [--help] <command> <argument>\n");
     fprintf(fp, "\n");
     fprintf(fp, "Commands:\n");
 
diff --git a/mcall.c b/mcall.c
index a6096d8..495f849 100644
--- a/mcall.c
+++ b/mcall.c
@@ -311,6 +311,7 @@ void mcall_destroy(call_t *call)
     free(call->gts); free(call->cgts); free(call->ugts);
     free(call->pdg);
     free(call->als);
+    free(call->ac);
     return;
 }
 
@@ -690,7 +691,7 @@ static void mcall_set_ref_genotypes(call_t *call, int nals)
     int ngts  = nals*(nals+1)/2;
     int nsmpl = bcf_hdr_nsamples(call->hdr);
 
-    for (i=0; i<4; i++) call->ac[i] = 0;
+    for (i=0; i<nals; i++) call->ac[i] = 0;
     call->nhets = 0;
     call->ndiploid = 0;
 
@@ -726,7 +727,7 @@ static void mcall_call_genotypes(call_t *call, bcf1_t *rec, int nals, int nout_a
     int nout_gts = nout_als*(nout_als+1)/2;
     hts_expand(float,nout_gts*nsmpl,call->nGPs,call->GPs);
 
-    for (i=0; i<4; i++) call->ac[i] = 0;
+    for (i=0; i<nout_als; i++) call->ac[i] = 0;
     call->nhets = 0;
     call->ndiploid = 0;
 
@@ -899,10 +900,11 @@ static void mcall_call_genotypes(call_t *call, bcf1_t *rec, int nals, int nout_a
 static void mcall_call_trio_genotypes(call_t *call, bcf1_t *rec, int nals, int nout_als, int out_als)
 {
     int ia, ib, i;
-    int nsmpl   = bcf_hdr_nsamples(call->hdr);
-    int ngts    = nals*(nals+1)/2;
-    double *gls = call->GLs - ngts;
-    double *pdg = call->pdg - ngts;
+    int nsmpl    = bcf_hdr_nsamples(call->hdr);
+    int ngts     = nals*(nals+1)/2;
+    int nout_gts = nout_als*(nout_als+1)/2;
+    double *gls  = call->GLs - nout_gts;
+    double *pdg  = call->pdg - ngts;
 
     // Calculate individuals' genotype likelihoods P(X=i)
     int isample;
@@ -911,19 +913,19 @@ static void mcall_call_trio_genotypes(call_t *call, bcf1_t *rec, int nals, int n
         int ploidy = call->ploidy ? call->ploidy[isample] : 2;
         int32_t *gts = call->ugts + isample;
 
-        gls += ngts;
+        gls += nout_gts;
         pdg += ngts;
 
         // Skip samples with all pdg's equal to 1. These have zero depth.
         for (i=0; i<ngts; i++) if ( pdg[i]!=0.0 ) break;
         if ( i==ngts || !ploidy )
         {
-            gts[0] = bcf_gt_missing;
+            gts[0] = -1;
             gls[0] = 1;
             continue;
         }
 
-        for (i=0; i<ngts; i++) gls[i] = -HUGE_VAL;
+        for (i=0; i<nout_gts; i++) gls[i] = -HUGE_VAL;
 
         double sum_lk  = 0;
         double best_lk = 0;
@@ -962,7 +964,7 @@ static void mcall_call_trio_genotypes(call_t *call, bcf1_t *rec, int nals, int n
                 }
             }
         }
-        for (i=0; i<ngts; i++)
+        for (i=0; i<nout_gts; i++)
             if ( gls[i]!=-HUGE_VAL ) gls[i] = log(gls[i]/sum_lk);
     }
 
@@ -1001,11 +1003,11 @@ static void mcall_call_trio_genotypes(call_t *call, bcf1_t *rec, int nals, int n
         for (i=0; i<3; i++)     // for father, mother, child
         {
             int ismpl = fam->sample[i];
-            double *gl = call->GLs + ngts*ismpl;
+            double *gl = call->GLs + nout_gts*ismpl;
             if ( gl[0]==1 ) continue;
             int j, jmax = 0;
             double max  = gl[0];
-            for (j=1; j<ngts; j++)
+            for (j=1; j<nout_gts; j++)
                 if ( max < gl[j] ) { max = gl[j]; jmax = j; }
             uc_lk += max;
             uc_itr |= jmax << ((2-i)*4);
@@ -1021,7 +1023,7 @@ static void mcall_call_trio_genotypes(call_t *call, bcf1_t *rec, int nals, int n
             for (i=0; i<3; i++)     // for father, mother, child
             {
                 int ismpl = fam->sample[i];
-                double *gl = call->GLs + ngts*ismpl;
+                double *gl = call->GLs + nout_gts*ismpl;
                 if ( gl[0]==1 ) continue;
                 int igt = trio[itr]>>((2-i)*4) & 0xf;
                 assert( !call->ploidy || call->ploidy[ismpl]>0 );
@@ -1041,10 +1043,10 @@ static void mcall_call_trio_genotypes(call_t *call, bcf1_t *rec, int nals, int n
         if ( !uc_is_mendelian )
         {
             uc_lk += log(1 - trio_Pm);
-            //fprintf(stderr,"c_lk=%e uc_lk=%e c_itr=%d%d%d uc_itr=%d%d%d\n", c_lk,uc_lk,c_itr>>8&0xf,c_itr>>4&0xf,c_itr&0xf,uc_itr>>8&0xf,uc_itr>>4&0xf,uc_itr&0xf);
+            // fprintf(stderr,"c_lk=%e uc_lk=%e c_itr=%d%d%d uc_itr=%d%d%d\n", c_lk,uc_lk,c_itr>>8&0xf,c_itr>>4&0xf,c_itr&0xf,uc_itr>>8&0xf,uc_itr>>4&0xf,uc_itr&0xf);
             if ( c_lk < uc_lk ) { c_lk = uc_lk; c_itr = uc_itr; }
         }
-        //fprintf(stderr,"best_lk=%e best_itr=%d%d%d uc_itr=%d%d%d\n", c_lk,c_itr>>8&0xf,c_itr>>4&0xf,c_itr&0xf,uc_itr>>8&0xf,uc_itr>>4&0xf,uc_itr&0xf);
+        // fprintf(stderr,"best_lk=%e best_itr=%d%d%d uc_itr=%d%d%d\n", c_lk,c_itr>>8&0xf,c_itr>>4&0xf,c_itr&0xf,uc_itr>>8&0xf,uc_itr>>4&0xf,uc_itr&0xf);
 
         // Set genotypes for father, mother, child and calculate genotype qualities
         for (i=0; i<3; i++)
@@ -1052,11 +1054,11 @@ static void mcall_call_trio_genotypes(call_t *call, bcf1_t *rec, int nals, int n
             // GT
             int ismpl    = fam->sample[i];
             int igt      = c_itr>>((2-i)*4) & 0xf;
-            double *gl   = call->GLs + ngts*ismpl;
+            double *gl   = call->GLs + nout_gts*ismpl;
             int32_t *gts = call->cgts + ismpl;
             if ( gl[0]==1 || igt==GT_SKIP )    // zero depth, set missing genotypes
             {
-                gts[0] = bcf_gt_missing;
+                gts[0] = -1;
                 // bcf_float_set_missing(call->GQs[ismpl]);
                 continue;
             }
@@ -1106,7 +1108,7 @@ static void mcall_call_trio_genotypes(call_t *call, bcf1_t *rec, int nals, int n
         cgts++;
         ugts++;
         gts += 2;
-        if ( bcf_gt_is_missing(ugts[0]) )
+        if ( ugts[0]==-1 )
         {
             gts[0] = bcf_gt_missing;
             gts[1] = ploidy==2 ? bcf_gt_missing : bcf_int32_vector_end;
@@ -1184,56 +1186,80 @@ void mcall_trim_numberR(call_t *call, bcf1_t *rec, int nals, int nout_als, int o
 {
     int i, ret;
 
-    // only DPR so far, we may generalize to arbitrary Number=R if necessary
-    ret = bcf_get_info_int32(call->hdr, rec, "DPR", &call->itmp, &call->n_itmp);
-    if ( ret>0 )
+    // at the moment we have DPR,AD,ADF,ADR all Number=R,Type=Integer,
+    // so only dealing with these cases at the moment
+    for (i=0; i<rec->n_info; i++)
     {
-        assert( ret==nals );
-        if ( out_als==1 )
-            bcf_update_info_int32(call->hdr, rec, "DPR", call->itmp, 1);
-        else
+        bcf_info_t *info = &rec->d.info[i];
+        int vlen = bcf_hdr_id2length(call->hdr,BCF_HL_INFO,info->key);
+        if ( vlen!=BCF_VL_R ) continue;
+        int type = bcf_hdr_id2type(call->hdr,BCF_HL_INFO,info->key);
+        if ( type!=BCF_HT_INT ) continue;
+
+        ret = bcf_get_info_int32(call->hdr, rec, bcf_hdr_int2id(call->hdr,BCF_DT_ID,info->key), &call->itmp, &call->n_itmp);
+        if ( ret>0 )
         {
-            for (i=0; i<nals; i++)
+            assert( ret==nals );
+            if ( out_als==1 )
+                bcf_update_info_int32(call->hdr, rec, bcf_hdr_int2id(call->hdr,BCF_DT_ID,info->key), call->itmp, 1);
+            else
             {
-                if ( call->als_map[i]==-1 ) continue;   // to be dropped
-                call->PLs[ call->als_map[i] ] = call->itmp[i]; // reusing PLs storage which is not used at this point
+                int j;
+                for (j=0; j<nals; j++)
+                {
+                    if ( call->als_map[j]==-1 ) continue;   // to be dropped
+                    call->PLs[ call->als_map[j] ] = call->itmp[j]; // reusing PLs storage which is not used at this point
+                }
+                bcf_update_info_int32(call->hdr, rec, bcf_hdr_int2id(call->hdr,BCF_DT_ID,info->key), call->PLs, nout_als);
             }
-            bcf_update_info_int32(call->hdr, rec, "DPR", call->PLs, nout_als);
         }
     }
 
-    ret = bcf_get_format_int32(call->hdr, rec, "DPR", &call->itmp, &call->n_itmp);
-    if ( ret>0 )
+    for (i=0; i<rec->n_fmt; i++)
     {
-        int nsmpl = bcf_hdr_nsamples(call->hdr);
-        int ndp = ret / nsmpl;
-        assert( ndp==nals );
-        if ( out_als==1 )
+        bcf_fmt_t *fmt = &rec->d.fmt[i];
+        int vlen = bcf_hdr_id2length(call->hdr,BCF_HL_FMT,fmt->id);
+        if ( vlen!=BCF_VL_R ) continue;
+        int type = bcf_hdr_id2type(call->hdr,BCF_HL_FMT,fmt->id);
+        if ( type!=BCF_HT_INT ) continue;
+
+        ret = bcf_get_format_int32(call->hdr, rec, bcf_hdr_int2id(call->hdr,BCF_DT_ID,fmt->id), &call->itmp, &call->n_itmp);
+        if ( ret>0 )
         {
-            for (i=0; i<nsmpl; i++)
-                call->PLs[i] = call->itmp[i*ndp];
+            int j, nsmpl = bcf_hdr_nsamples(call->hdr);
+            int ndp = ret / nsmpl;
+            assert( ndp==nals );
+            if ( out_als==1 )
+            {
+                for (j=0; j<nsmpl; j++)
+                    call->PLs[j] = call->itmp[j*ndp];
 
-            bcf_update_format_int32(call->hdr, rec, "DPR", call->PLs, nsmpl);
-        }
-        else
-        {
-            int j;
-            for (i=0; i<nsmpl; i++)
+                bcf_update_format_int32(call->hdr, rec, bcf_hdr_int2id(call->hdr,BCF_DT_ID,fmt->id), call->PLs, nsmpl);
+            }
+            else
             {
-                int32_t *dp_dst = call->PLs + i*nout_als;
-                int32_t *dp_src = call->itmp + i*ndp;
-                for (j=0; j<nals; j++)
+                int k;
+                for (j=0; j<nsmpl; j++)
                 {
-                    if ( call->als_map[j]==-1 ) continue;   // to be dropped
-                    dp_dst[ call->als_map[j] ] = dp_src[j]; // reusing PLs storage which is not used at this point
+                    int32_t *dp_dst = call->PLs + j*nout_als;
+                    int32_t *dp_src = call->itmp + j*ndp;
+                    for (k=0; k<nals; k++)
+                    {
+                        if ( call->als_map[k]==-1 ) continue;   // to be dropped
+                        dp_dst[ call->als_map[k] ] = dp_src[k]; // reusing PLs storage which is not used at this point
+                    }
                 }
+                bcf_update_format_int32(call->hdr, rec, bcf_hdr_int2id(call->hdr,BCF_DT_ID,fmt->id), call->PLs, nsmpl*nout_als);
             }
-            bcf_update_format_int32(call->hdr, rec, "DPR", call->PLs, nsmpl*nout_als);
         }
     }
 }
 
-static void mcall_constrain_alleles(call_t *call, bcf1_t *rec, int unseen)
+
+// NB: in this function we temporarily use calls->als_map for a different
+// purpose to store mapping from new (target) alleles to original alleles.
+//
+static void mcall_constrain_alleles(call_t *call, bcf1_t *rec, int *unseen)
 {
     bcf_sr_regions_t *tgt = call->srs->targets;
     if ( tgt->nals>5 ) error("Maximum accepted number of alleles is 5, got %d\n", tgt->nals);
@@ -1256,6 +1282,8 @@ static void mcall_constrain_alleles(call_t *call, bcf1_t *rec, int unseen)
         call->als[nals] = tgt->als[i];
         j = vcmp_find_allele(call->vcmp, rec->d.allele+1, rec->n_allele - 1, tgt->als[i]);
 
+        if ( j+1==*unseen ) error("Cannot constrain to %s\n",tgt->als[i]);
+        
         if ( j>=0 )
         {
             // existing allele
@@ -1268,11 +1296,18 @@ static void mcall_constrain_alleles(call_t *call, bcf1_t *rec, int unseen)
             // present at multiallelic indels sites. In that case we use the
             // last allele anyway, because the least likely allele comes last
             // in mpileup's ALT output.
-            call->als_map[nals] = unseen>=0 ? unseen : rec->n_allele - 1;
+            call->als_map[nals] = (*unseen)>=0 ? *unseen : rec->n_allele - 1;
             has_new = 1;
         }
         nals++;
     }
+    if ( *unseen )
+    {
+        call->als_map[nals] = *unseen;
+        call->als[nals] = rec->d.allele[*unseen];
+        nals++;
+    }
+
     if ( !has_new && nals==rec->n_allele ) return;
     bcf_update_alleles(call->hdr, rec, (const char**)call->als, nals);
 
@@ -1299,17 +1334,18 @@ static void mcall_constrain_alleles(call_t *call, bcf1_t *rec, int unseen)
         for (k=0; k<npls_new; k++)
         {
             new_pl[k] = ori_pl[call->pl_map[k]];
-            if ( new_pl[k]==bcf_int32_missing && unseen>=0 )
+            if ( new_pl[k]==bcf_int32_missing && *unseen>=0 )
             {
                 // missing value, and there is an unseen allele: identify the
                 // alleles and use the lk of either AX or XX
                 int k_ori = call->pl_map[k], ia, ib;
                 bcf_gt2alleles(k_ori, &ia, &ib);
-                k_ori = bcf_alleles2gt(ia,unseen);
-                if ( ori_pl[k_ori]==bcf_int32_missing ) k_ori = bcf_alleles2gt(ib,unseen);
-                if ( ori_pl[k_ori]==bcf_int32_missing ) k_ori = bcf_alleles2gt(unseen,unseen);
+                k_ori = bcf_alleles2gt(ia,*unseen);
+                if ( ori_pl[k_ori]==bcf_int32_missing ) k_ori = bcf_alleles2gt(ib,*unseen);
+                if ( ori_pl[k_ori]==bcf_int32_missing ) k_ori = bcf_alleles2gt(*unseen,*unseen);
                 new_pl[k] = ori_pl[k_ori];
             }
+            if ( !k && new_pl[k]==bcf_int32_vector_end ) new_pl[k]=bcf_int32_missing;
         }
         ori_pl += npls_ori;
         new_pl += npls_new;
@@ -1322,6 +1358,8 @@ static void mcall_constrain_alleles(call_t *call, bcf1_t *rec, int unseen)
     for (i=0; i<nals; i++)
         qsum[i] = call->als_map[i]<nqs ? call->qsum[call->als_map[i]] : 0;
     bcf_update_info_float(call->hdr, rec, "QS", qsum, nals);
+
+    if ( *unseen ) *unseen = nals-1;
 }
 
 
@@ -1333,19 +1371,14 @@ static void mcall_constrain_alleles(call_t *call, bcf1_t *rec, int unseen)
   */
 int mcall(call_t *call, bcf1_t *rec)
 {
-    int i, unseen = -1;
-    for (i=1; i<rec->n_allele; i++)
-    {
-        if ( rec->d.allele[i][0]=='X' ) { unseen = i; break; }  // old X
-        if ( rec->d.allele[i][0]=='<' && rec->d.allele[i][1]=='X' && rec->d.allele[i][1]=='>' ) { unseen = i; break; } // old <X>
-        if ( rec->d.allele[i][0]=='<' && rec->d.allele[i][1]=='*' && rec->d.allele[i][1]=='>' ) { unseen = i; break; } // new <*>
-    }
+    int i, unseen = call->unseen;
 
     // Force alleles when calling genotypes given alleles was requested
-    if ( call->flag & CALL_CONSTR_ALLELES ) mcall_constrain_alleles(call, rec, unseen);
+    if ( call->flag & CALL_CONSTR_ALLELES ) mcall_constrain_alleles(call, rec, &unseen);
 
     int nsmpl = bcf_hdr_nsamples(call->hdr);
     int nals  = rec->n_allele;
+    hts_expand(int,nals,call->nac,call->ac);
     hts_expand(int,nals,call->nals_map,call->als_map);
     hts_expand(int,nals*(nals+1)/2,call->npl_map,call->pl_map);
 
@@ -1391,7 +1424,13 @@ int mcall(call_t *call, bcf1_t *rec)
     #endif
 
     // Find the best combination of alleles
-    int out_als, nout = mcall_find_best_alleles(call, nals, &out_als);
+    int out_als, nout;
+    if ( nals > 8*sizeof(out_als) )
+    { 
+        fprintf(stderr,"Too many alleles at %s:%d, skipping.\n", bcf_seqname(call->hdr,rec),rec->pos+1); 
+        return 0; 
+    }
+    nout = mcall_find_best_alleles(call, nals, &out_als);
 
     // Make sure the REF allele is always present
     if ( !(out_als&1) )
@@ -1408,9 +1447,7 @@ int mcall(call_t *call, bcf1_t *rec)
         nout = 0;
         for (i=0; i<nals; i++)
         {
-            if ( rec->d.allele[i][0]=='X' ) continue;   // old version of unseen allele "X"
-            if ( rec->d.allele[i][0]=='<' && rec->d.allele[i][1]=='X' && rec->d.allele[i][2]=='>' ) continue;   // old version of unseen allele, "<X>"
-            if ( rec->d.allele[i][0]=='<' && rec->d.allele[i][1]=='*' && rec->d.allele[i][2]=='>' ) continue;   // new version of unseen allele, "<*>"
+            if ( i>0 && i==unseen ) continue;
             out_als |= 1<<i;
             nout++;
         }
@@ -1431,12 +1468,20 @@ int mcall(call_t *call, bcf1_t *rec)
         if ( !is_variant )
             mcall_set_ref_genotypes(call,nals);     // running with -A, prevent mcall_call_genotypes from putting some ALT back
         else if ( call->flag & CALL_CONSTR_TRIO )
+        {
+            if ( nout>4 ) 
+            { 
+                fprintf(stderr,"Too many alleles at %s:%d, skipping.\n", bcf_seqname(call->hdr,rec),rec->pos+1); 
+                return 0; 
+            }
             mcall_call_trio_genotypes(call, rec, nals,nout,out_als);
+        }
         else
             mcall_call_genotypes(call,rec,nals,nout,out_als);
 
         // Skip the site if all samples are 0/0. This can happen occasionally.
-        nAC = call->ac[1] + call->ac[2] + call->ac[3];
+        nAC = 0;
+        for (i=1; i<nout; i++) nAC += call->ac[i];
         if ( !nAC && call->flag & CALL_VARONLY ) return 0;
         mcall_trim_PLs(call, rec, nals, nout, out_als);
     }
@@ -1452,12 +1497,12 @@ int mcall(call_t *call, bcf1_t *rec)
         if ( hob != HUGE_VAL ) bcf_update_info_float(call->hdr, rec, "HOB", &hob, 1);
 
         // Quality of a variant site. fabs() to avoid negative zeros in VCF output when CALL_KEEPALT is set
-        rec->qual = call->lk_sum==-HUGE_VAL ? 0 : fabs(-4.343*(call->ref_lk - call->lk_sum));
+        rec->qual = call->lk_sum==-HUGE_VAL || call->ref_lk==0 ? 0 : fabs(-4.343*(call->ref_lk - call->lk_sum));
     }
     else
     {
         // Set the quality of a REF site
-        rec->qual = call->lk_sum==-HUGE_VAL ? 0 : -4.343*log(1 - exp(call->ref_lk - call->lk_sum));
+        rec->qual = call->lk_sum==-HUGE_VAL || call->ref_lk==0 ? 0 : -4.343*log(1 - exp(call->ref_lk - call->lk_sum));
     }
     if ( rec->qual>999 ) rec->qual = 999;
     if ( rec->qual>50 ) rec->qual = rint(rec->qual);
@@ -1475,13 +1520,14 @@ int mcall(call_t *call, bcf1_t *rec)
     bcf_update_genotypes(call->hdr, rec, call->gts, nsmpl*2);
 
     // DP4 tag
-    if ( bcf_get_info_float(call->hdr, rec, "I16", &call->anno16, &call->n16)!=16 )
-        error("I16 hasn't 16 fields at %s:%d\n", call->hdr->id[BCF_DT_CTG][rec->rid].key,rec->pos+1);
-    int32_t dp[4]; dp[0] = call->anno16[0]; dp[1] = call->anno16[1]; dp[2] = call->anno16[2]; dp[3] = call->anno16[3];
-    bcf_update_info_int32(call->hdr, rec, "DP4", dp, 4);
+    if ( bcf_get_info_float(call->hdr, rec, "I16", &call->anno16, &call->n16)==16 )
+    {
+        int32_t dp[4]; dp[0] = call->anno16[0]; dp[1] = call->anno16[1]; dp[2] = call->anno16[2]; dp[3] = call->anno16[3];
+        bcf_update_info_int32(call->hdr, rec, "DP4", dp, 4);
 
-    int32_t mq = (call->anno16[8]+call->anno16[10])/(call->anno16[0]+call->anno16[1]+call->anno16[2]+call->anno16[3]);
-    bcf_update_info_int32(call->hdr, rec, "MQ", &mq, 1);
+        int32_t mq = (call->anno16[8]+call->anno16[10])/(call->anno16[0]+call->anno16[1]+call->anno16[2]+call->anno16[3]);
+        bcf_update_info_int32(call->hdr, rec, "MQ", &mq, 1);
+    }
 
     bcf_update_info_int32(call->hdr, rec, "I16", NULL, 0);     // remove I16 tag
     bcf_update_info_int32(call->hdr, rec, "QS", NULL, 0);      // remove QS tag
diff --git a/peakfit.c b/peakfit.c
new file mode 100644
index 0000000..2bc8492
--- /dev/null
+++ b/peakfit.c
@@ -0,0 +1,599 @@
+/* The MIT License
+
+   Copyright (c) 2013-2015 Genome Research Ltd.
+
+   Author: Petr Danecek <pd3 at sanger.ac.uk>
+   
+   Permission is hereby granted, free of charge, to any person obtaining a copy
+   of this software and associated documentation files (the "Software"), to deal
+   in the Software without restriction, including without limitation the rights
+   to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+   copies of the Software, and to permit persons to whom the Software is
+   furnished to do so, subject to the following conditions:
+   
+   The above copyright notice and this permission notice shall be included in
+   all copies or substantial portions of the Software.
+   
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+   IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+   FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+   AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+   LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+   OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+   THE SOFTWARE.
+
+ */
+
+#include "peakfit.h"
+#include <stdio.h>
+#include <gsl/gsl_vector.h>
+#include <gsl/gsl_multifit_nlin.h>
+#include <htslib/hts.h>
+#include <htslib/kstring.h>
+#include <assert.h>
+#include <math.h>
+
+#define NPARAMS 5
+
+// gauss params: sqrt(scale), center, sigma
+typedef struct _peak_t
+{
+    int fit_mask;
+    double params[NPARAMS], ori_params[NPARAMS];    // current and input parameters
+    struct { int scan; double min, max, best; } mc[NPARAMS];    // monte-carlo settings and best parameter
+    void (*calc_f)  (int nvals, double *xvals, double *yvals, void *args);
+    void (*calc_df) (int nvals, double *xvals, double *yvals, double *dfvals, int idf, void *args);
+    void (*print_func) (struct _peak_t *pk, kstring_t *str);
+    void (*convert_get) (struct _peak_t *pk, double *params);
+    double (*convert_set) (struct _peak_t *pk, int iparam, double value);
+}
+peak_t;
+
+struct _peakfit_t
+{
+    int npeaks, mpeaks, nparams, mparams;
+    peak_t *peaks;
+    double *params;
+    int nvals, mvals;
+    double *xvals, *yvals, *vals;
+    kstring_t str;
+    int verbose, nmc_iter;
+};
+
+
+/*
+    Gaussian peak with the center bound in the interval <d,e>:
+        yi = scale^2 * exp(-(xi-z)^2/sigma^2)
+
+        dy/dscale  = 2*scale * EXP
+        dy/dcenter = -scale^2 * sin(center) * (e-d) * (xi - z) * EXP / sigma^2
+        dy/dsigma  = 2*scale^2 * (xi - z)^2 * EXP / sigma^3
+
+    where
+        z   = 0.5*(cos(center)+1)*(e-d) + d
+        EXP = exp(-(xi-z)^2/sigma^2)
+*/
+void bounded_gaussian_calc_f(int nvals, double *xvals, double *yvals, void *args)
+{
+    peak_t *pk = (peak_t*) args;
+
+    double scale2 = pk->params[0] * pk->params[0];
+    double center = pk->params[1];
+    double sigma  = pk->params[2];
+    double d = pk->params[3];
+    double e = pk->params[4];
+    double z = 0.5*(cos(center)+1)*(e-d) + d;
+
+    int i;
+    for (i=0; i<nvals; i++)
+    {
+        double tmp = (xvals[i] - z)/sigma;
+        yvals[i] += scale2 * exp(-tmp*tmp);
+    }
+}
+void bounded_gaussian_calc_df(int nvals, double *xvals, double *yvals, double *dfvals, int idf, void *args)
+{
+    peak_t *pk = (peak_t*) args;
+
+    double scale  = pk->params[0];
+    double center = pk->params[1];
+    double sigma  = pk->params[2];
+    double d = pk->params[3];
+    double e = pk->params[4];
+    double z = 0.5*(cos(center)+1)*(e-d) + d;
+
+    int i;
+    for (i=0; i<nvals; i++)
+    {
+        double EXP = exp(-(xvals[i]-z)*(xvals[i]-z)/sigma/sigma);
+        double zi  = xvals[i] - z;
+        if ( idf==0 )       // dscale
+            dfvals[i] += 2*scale*EXP;
+        else if ( idf==1 )  // dcenter
+            dfvals[i] -= scale*scale*sin(center)*(e-d)*zi*EXP/sigma/sigma;
+        else if ( idf==2 )  // dsigma
+            dfvals[i] += 2*scale*scale*zi*zi*EXP/sigma/sigma/sigma;
+    }
+}
+void bounded_gaussian_sprint_func(peak_t *pk, kstring_t *str)
+{
+    double center = pk->params[1];
+    double d = pk->params[3];
+    double e = pk->params[4];
+    double z = 0.5*(cos(center)+1)*(e-d) + d;
+    ksprintf(str,"%f**2 * exp(-(x-%f)**2/%f**2)",fabs(pk->params[0]),z,fabs(pk->params[2]));
+}
+double bounded_gaussian_convert_set(peak_t *pk, int iparam, double value)
+{
+    if ( iparam!=1 ) return value;
+    double d = pk->ori_params[3];
+    double e = pk->ori_params[4];
+    if ( value<d ) value = d;
+    else if ( value>e ) value = e;
+    return acos(2*(value-d)/(e-d) - 1);
+}
+void bounded_gaussian_convert_get(peak_t *pk, double *params)
+{
+    params[0] = fabs(pk->params[0]);
+    params[2] = fabs(pk->params[2]);
+    double center = pk->params[1];
+    double d = pk->params[3];
+    double e = pk->params[4];
+    params[1] = 0.5*(cos(center)+1)*(e-d) + d;
+}
+
+void peakfit_add_bounded_gaussian(peakfit_t *pkf, double a, double b, double c, double d, double e, int fit_mask)
+{
+    pkf->npeaks++;
+    hts_expand0(peak_t,pkf->npeaks,pkf->mpeaks,pkf->peaks);
+
+    int i, nfit = 0;
+    for (i=0; i<NPARAMS; i++) 
+        if ( fit_mask & (1<<i) ) nfit++;
+
+    assert( d<e );
+
+    pkf->nparams += nfit;
+    hts_expand0(double,pkf->nparams,pkf->mparams,pkf->params);
+
+    peak_t *pk = &pkf->peaks[pkf->npeaks-1];
+    memset(pk, 0, sizeof(peak_t));
+
+    pk->calc_f      = bounded_gaussian_calc_f;
+    pk->calc_df     = bounded_gaussian_calc_df;
+    pk->print_func  = bounded_gaussian_sprint_func;
+    pk->convert_set = bounded_gaussian_convert_set;
+    pk->convert_get = bounded_gaussian_convert_get;
+    pk->fit_mask    = fit_mask;
+    pk->ori_params[0] = a;
+    pk->ori_params[2] = c;
+    pk->ori_params[3] = d;
+    pk->ori_params[4] = e;
+    pk->ori_params[1] = pk->convert_set(pk, 1, b);
+}
+
+
+/*
+    Gaussian peak:
+        yi = scale^2 * exp(-(x-center)^2/sigma^2)
+
+        dy/dscale  = 2 * scale * EXP
+        dy/dcenter = 2 * scale^2 * (x-center) * EXP / sigma^2
+        dy/dsigma  = 2 * scale^2 * (x-center)^2 * EXP / sigma^3
+
+    where 
+        EXP = exp(-(x-center)^2/sigma^2)
+*/
+void gaussian_calc_f(int nvals, double *xvals, double *yvals, void *args)
+{
+    peak_t *pk = (peak_t*) args;
+
+    double scale2 = pk->params[0] * pk->params[0];
+    double center = pk->params[1];
+    double sigma  = pk->params[2];
+
+    int i;
+    for (i=0; i<nvals; i++)
+    {
+        double tmp = (xvals[i] - center)/sigma;
+        yvals[i] += scale2 * exp(-tmp*tmp);
+    }
+}
+void gaussian_calc_df(int nvals, double *xvals, double *yvals, double *dfvals, int idf, void *args)
+{
+    peak_t *pk = (peak_t*) args;
+
+    double scale  = pk->params[0];
+    double center = pk->params[1];
+    double sigma  = pk->params[2];
+
+    int i;
+    for (i=0; i<nvals; i++)
+    {
+        double zi  = xvals[i] - center;
+        double EXP = exp(-zi*zi/(sigma*sigma));
+        if ( idf==0 )       // dscale
+            dfvals[i] += 2*scale*EXP;
+        else if ( idf==1 )  // dcenter
+            dfvals[i] += 2*scale*scale*zi*EXP/(sigma*sigma);
+        else if ( idf==2 )  // dsigma
+            dfvals[i] += 2*scale*scale*zi*zi*EXP/(sigma*sigma*sigma);
+    }
+}
+void gaussian_sprint_func(struct _peak_t *pk, kstring_t *str)
+{
+    ksprintf(str,"%f**2 * exp(-(x-%f)**2/%f**2)",fabs(pk->params[0]),pk->params[1],fabs(pk->params[2]));
+}
+void gaussian_convert_get(peak_t *pk, double *params)
+{
+    params[0] = fabs(pk->params[0]);
+    params[1] = fabs(pk->params[1]);
+    params[2] = fabs(pk->params[2]);
+}
+
+
+void peakfit_add_gaussian(peakfit_t *pkf, double a, double b, double c, int fit_mask)
+{
+    pkf->npeaks++;
+    hts_expand0(peak_t,pkf->npeaks,pkf->mpeaks,pkf->peaks);
+
+    int i, nfit = 0;
+    for (i=0; i<NPARAMS; i++) 
+        if ( fit_mask & (1<<i) ) nfit++;
+
+    pkf->nparams += nfit;
+    hts_expand0(double,pkf->nparams,pkf->mparams,pkf->params);
+
+    peak_t *pk = &pkf->peaks[pkf->npeaks-1];
+    memset(pk, 0, sizeof(peak_t));
+
+    pk->calc_f      = gaussian_calc_f;
+    pk->calc_df     = gaussian_calc_df;
+    pk->print_func  = gaussian_sprint_func;
+    pk->convert_get = gaussian_convert_get;
+    pk->fit_mask    = fit_mask;
+    pk->ori_params[0] = a;
+    pk->ori_params[1] = b;
+    pk->ori_params[2] = c;
+}
+
+
+/*
+    exp peak:
+        yi = scale^2 * exp((x-center)/sigma^2)
+
+        dy/dscale  = 2 * scale * EXP
+        dy/dcenter = -scale^2  * EXP / sigma^2
+        dy/dsigma  = -2 * scale^2 * (x-center) * EXP / sigma^3
+
+    where 
+        EXP = exp((x-center)/sigma^2)
+*/
+void exp_calc_f(int nvals, double *xvals, double *yvals, void *args)
+{
+    peak_t *pk = (peak_t*) args;
+
+    double scale2 = pk->params[0] * pk->params[0];
+    double center = pk->params[1];
+    double sigma  = pk->params[2];
+
+    int i;
+    for (i=0; i<nvals; i++)
+    {
+        yvals[i] += scale2 * exp((xvals[i]-center)/sigma/sigma);
+    }
+}
+void exp_calc_df(int nvals, double *xvals, double *yvals, double *dfvals, int idf, void *args)
+{
+    peak_t *pk = (peak_t*) args;
+
+    double scale  = pk->params[0];
+    double center = pk->params[1];
+    double sigma  = pk->params[2];
+
+    int i;
+    for (i=0; i<nvals; i++)
+    {
+        double EXP = exp((xvals[i]-center)/sigma/sigma);
+        if ( idf==0 )       // dscale
+            dfvals[i] += 2*scale*EXP;
+        else if ( idf==2 )  // dsigma
+            dfvals[i] -= 2*scale*scale*(xvals[i]-center)*EXP/sigma/sigma/sigma;
+    }
+}
+void exp_sprint_func(struct _peak_t *pk, kstring_t *str)
+{
+    ksprintf(str,"%f**2 * exp((x-%f)/%f**2)",fabs(pk->params[0]),pk->params[1],fabs(pk->params[2]));
+}
+void exp_convert_get(peak_t *pk, double *params)
+{
+    params[0] = fabs(pk->params[0]);
+    params[1] = fabs(pk->params[1]);
+    params[2] = fabs(pk->params[2]);
+}
+
+void peakfit_add_exp(peakfit_t *pkf, double a, double b, double c, int fit_mask)
+{
+    pkf->npeaks++;
+    hts_expand0(peak_t,pkf->npeaks,pkf->mpeaks,pkf->peaks);
+
+    int i, nfit = 0;
+    for (i=0; i<NPARAMS; i++) 
+        if ( fit_mask & (1<<i) ) nfit++;
+
+    assert( !(fit_mask&2) );
+
+    pkf->nparams += nfit;
+    hts_expand0(double,pkf->nparams,pkf->mparams,pkf->params);
+
+    peak_t *pk = &pkf->peaks[pkf->npeaks-1];
+    memset(pk, 0, sizeof(peak_t));
+
+    pk->calc_f      = exp_calc_f;
+    pk->calc_df     = exp_calc_df;
+    pk->print_func  = exp_sprint_func;
+    pk->convert_get = exp_convert_get;
+    pk->fit_mask    = fit_mask;
+    pk->ori_params[0] = a;
+    pk->ori_params[1] = b;
+    pk->ori_params[2] = c;
+}
+
+
+void peakfit_set_params(peakfit_t *pkf, int ipk, double *params, int nparams)
+{
+    peak_t *pk = &pkf->peaks[ipk];
+    int i;
+    if ( pk->convert_set )
+        for (i=0; i<nparams; i++) pk->params[i] = pk->convert_set(pk, i, params[i]);
+    else
+        for (i=0; i<nparams; i++) pk->params[i] = params[i];
+}
+
+void peakfit_get_params(peakfit_t *pkf, int ipk, double *params, int nparams)
+{
+    peak_t *pk = &pkf->peaks[ipk];
+    if ( pk->convert_get ) pk->convert_get(pk, params);
+    else
+    {
+        int i;
+        for (i=0; i<nparams; i++) params[i] = pk->params[i];
+    }
+}
+
+peakfit_t *peakfit_init(void)
+{
+    return (peakfit_t*)calloc(1,sizeof(peakfit_t));
+}
+
+void peakfit_reset(peakfit_t *pkf)
+{
+    pkf->npeaks = pkf->nparams = 0;
+    memset(pkf->peaks,0,sizeof(peak_t)*pkf->mpeaks);
+}
+
+void peakfit_destroy(peakfit_t *pkf)
+{
+    free(pkf->str.s);
+    free(pkf->vals);
+    free(pkf->params);
+    free(pkf->peaks);
+    free(pkf);
+}
+
+int peakfit_calc_f(const gsl_vector *params, void *data, gsl_vector *yvals)
+{
+    peakfit_t *pkf = (peakfit_t *) data;
+
+    int i,j;
+    for (i=0; i<pkf->nvals; i++)
+        pkf->vals[i] = 0;
+
+    int iparam = 0;
+    for (i=0; i<pkf->npeaks; i++)
+    {
+        peak_t *pk = &pkf->peaks[i];
+        for (j=0; j<NPARAMS; j++)
+        {
+            if ( !(pk->fit_mask & (1<<j)) ) continue;
+            pk->params[j] = gsl_vector_get(params,iparam);
+            iparam++;
+        }
+        pk->calc_f(pkf->nvals, pkf->xvals, pkf->vals, pk);
+    }
+
+    for (i=0; i<pkf->nvals; i++)
+        gsl_vector_set(yvals, i, (pkf->vals[i] - pkf->yvals[i])/0.01);
+
+    return GSL_SUCCESS;
+}
+int peakfit_calc_df(const gsl_vector *params, void *data, gsl_matrix *jacobian)
+{
+    peakfit_t *pkf = (peakfit_t *) data;
+
+    int i,j,k,iparam = 0;
+    for (i=0; i<pkf->npeaks; i++)
+    {
+        peak_t *pk = &pkf->peaks[i];
+        int iparam_prev = iparam;
+        for (j=0; j<NPARAMS; j++)
+        {
+            if ( !(pk->fit_mask & (1<<j)) ) continue;
+            pk->params[j] = gsl_vector_get(params,iparam);
+            iparam++;
+        }
+        iparam = iparam_prev;
+        for (j=0; j<NPARAMS; j++)
+        {
+            if ( !(pk->fit_mask & (1<<j)) ) continue;
+            for (k=0; k<pkf->nvals; k++) pkf->vals[k] = 0;
+            pk->calc_df(pkf->nvals, pkf->xvals, pkf->yvals, pkf->vals, j, pk);
+            for (k=0; k<pkf->nvals; k++) gsl_matrix_set(jacobian, k, iparam, pkf->vals[k]);
+            iparam++;
+        }
+    }
+    return GSL_SUCCESS;
+}
+int peakfit_calc_fdf(const gsl_vector *params, void *data, gsl_vector *yvals, gsl_matrix *jacobian)
+{
+    peakfit_calc_f(params, data, yvals);
+    peakfit_calc_df(params, data, jacobian);
+    return GSL_SUCCESS;
+}
+
+double peakfit_evaluate(peakfit_t *pkf)
+{
+    int i;
+    for (i=0; i<pkf->nvals; i++)
+        pkf->vals[i] = 0;
+
+    for (i=0; i<pkf->npeaks; i++)
+        pkf->peaks[i].calc_f(pkf->nvals, pkf->xvals, pkf->vals, &pkf->peaks[i]);
+
+    double sum = 0;
+    for (i=0; i<pkf->nvals; i++)
+        sum += fabs(pkf->vals[i] - pkf->yvals[i]);
+
+    return sum;
+}
+
+const char *peakfit_sprint_func(peakfit_t *pkf)
+{
+    pkf->str.l = 0;
+    int i;
+    for (i=0; i<pkf->npeaks; i++)
+    {
+        if ( i>0 ) kputs(" + ", &pkf->str);
+        pkf->peaks[i].print_func(&pkf->peaks[i], &pkf->str);
+    }
+    return (const char*)pkf->str.s;
+}
+
+void peakfit_verbose(peakfit_t *pkf, int level)
+{
+    pkf->verbose = level;
+}
+
+void peakfit_set_mc(peakfit_t *pkf, double xmin, double xmax, int iparam, int niter)
+{
+    peak_t *pk = &pkf->peaks[ pkf->npeaks-1 ];
+    pk->mc[iparam].scan = 1;
+    pk->mc[iparam].min  = xmin;
+    pk->mc[iparam].max  = xmax;
+    pkf->nmc_iter = niter;
+}
+
+double peakfit_run(peakfit_t *pkf, int nvals, double *xvals, double *yvals)
+{
+    srand(0);   // for reproducibility
+
+    pkf->nvals = nvals;
+    pkf->xvals = xvals;
+    pkf->yvals = yvals;
+    hts_expand0(double,pkf->nvals,pkf->mvals,pkf->vals);
+    if ( !pkf->nparams ) return peakfit_evaluate(pkf);
+
+    gsl_multifit_function_fdf mfunc;
+    mfunc.f   = &peakfit_calc_f;
+    mfunc.df  = &peakfit_calc_df;
+    mfunc.fdf = &peakfit_calc_fdf;
+    mfunc.n   = nvals;
+    mfunc.p   = pkf->nparams;
+    mfunc.params = pkf;
+
+    const gsl_multifit_fdfsolver_type *solver_type;
+    gsl_multifit_fdfsolver *solver;
+    solver_type = gsl_multifit_fdfsolver_lmsder;
+    solver = gsl_multifit_fdfsolver_alloc(solver_type, nvals, mfunc.p);
+    gsl_vector *grad = gsl_vector_alloc(pkf->nparams);
+
+    int imc_iter, i,j, iparam;
+    double best_fit = HUGE_VAL;
+    for (imc_iter=0; imc_iter<=pkf->nmc_iter; imc_iter++)   // possibly multiple monte-carlo iterations
+    {
+        // set GSL parameters
+        iparam = 0;
+        for (i=0; i<pkf->npeaks; i++)
+        {
+            peak_t *pk = &pkf->peaks[i];
+            for (j=0; j<NPARAMS; j++)
+            {
+                pk->params[j] = pk->ori_params[j];
+                if ( pk->mc[j].scan )
+                {
+                    pk->params[j] = rand()*(pk->mc[j].max - pk->mc[j].min)/RAND_MAX + pk->mc[j].min;
+                    if ( pk->convert_set ) pk->params[j] = pk->convert_set(pk, j, pk->params[j]);
+                }
+                if ( !(pk->fit_mask & (1<<j)) ) continue;
+                pkf->params[iparam] = pk->params[j];
+                iparam++;
+            }
+        }
+
+        gsl_vector_view vview = gsl_vector_view_array(pkf->params, mfunc.p);
+        gsl_multifit_fdfsolver_set(solver, &mfunc, &vview.vector);
+
+        // iterate until convergence (or lack of it)
+        int ret, test1 = 0, test2 = 0, niter = 0, niter_max = 500;
+        do
+        {
+            ret = gsl_multifit_fdfsolver_iterate(solver);
+            if ( pkf->verbose >1 )
+            {
+                fprintf(stderr, "%d: ", niter);
+                for (i=0; i<pkf->npeaks; i++)
+                {
+                    peak_t *pk = &pkf->peaks[i];
+                    fprintf(stderr,"\t%f %f %f", pk->params[0],pk->params[1],pk->params[2]);
+                }
+                fprintf(stderr, "\t.. %s\n", gsl_strerror(ret));
+            }
+            if ( ret ) break;
+
+            gsl_multifit_gradient(solver->J, solver->f, grad);
+            test1 = gsl_multifit_test_gradient(grad, 1e-8);
+            test2 = gsl_multifit_test_delta(solver->dx, solver->x, 1e-8, 1e-8);
+        }
+        while ((test1==GSL_CONTINUE || test2==GSL_CONTINUE) && ++niter<niter_max);
+        if ( pkf->verbose >1 )
+        {
+            fprintf(stderr,"test1=%s\n", gsl_strerror(test1));
+            fprintf(stderr,"test2=%s\n", gsl_strerror(test2));
+        }
+
+        // recover parameters
+        iparam = 0;
+        for (i=0; i<pkf->npeaks; i++)
+        {
+            peak_t *pk = &pkf->peaks[i];
+            for (j=0; j<NPARAMS; j++)
+            {
+                if ( !(pk->fit_mask & (1<<j)) ) continue;
+                pk->params[j] = gsl_vector_get(solver->x, iparam++);
+            }
+        }
+
+        // evaluate fit, update best parameters
+        double fit = peakfit_evaluate(pkf);
+        if ( fit<best_fit )
+        {
+            for (i=0; i<pkf->npeaks; i++)
+            {
+                peak_t *pk = &pkf->peaks[i];
+                for (j=0; j<NPARAMS; j++) pk->mc[j].best = pk->params[j];
+            }
+        }
+        if ( fit<best_fit ) best_fit = fit;
+    }
+    gsl_multifit_fdfsolver_free(solver);
+    gsl_vector_free(grad);
+
+    for (i=0; i<pkf->npeaks; i++)
+    {
+        peak_t *pk = &pkf->peaks[i];
+        for (j=0; j<NPARAMS; j++) pk->params[j] = pk->mc[j].best;
+    }
+    return best_fit;
+}
+
+
diff --git a/peakfit.h b/peakfit.h
new file mode 100644
index 0000000..8a9e4fa
--- /dev/null
+++ b/peakfit.h
@@ -0,0 +1,49 @@
+/* The MIT License
+
+   Copyright (c) 2013-2015 Genome Research Ltd.
+
+   Author: Petr Danecek <pd3 at sanger.ac.uk>
+   
+   Permission is hereby granted, free of charge, to any person obtaining a copy
+   of this software and associated documentation files (the "Software"), to deal
+   in the Software without restriction, including without limitation the rights
+   to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+   copies of the Software, and to permit persons to whom the Software is
+   furnished to do so, subject to the following conditions:
+   
+   The above copyright notice and this permission notice shall be included in
+   all copies or substantial portions of the Software.
+   
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+   IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+   FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+   AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+   LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+   OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+   THE SOFTWARE.
+
+ */
+
+#ifndef PEAKFIT_H
+#define PEAKFIT_H
+
+typedef struct _peakfit_t peakfit_t;
+
+peakfit_t *peakfit_init(void);
+void peakfit_reset(peakfit_t *pkf);
+void peakfit_destroy(peakfit_t *pkf);
+
+void peakfit_add_gaussian(peakfit_t *pkf, double a, double b, double c, int fit_mask);
+void peakfit_add_bounded_gaussian(peakfit_t *pkf, double a, double b, double c, double d, double e, int fit_mask);
+void peakfit_add_exp(peakfit_t *pkf, double a, double b, double c, int fit_mask);
+void peakfit_set_mc(peakfit_t *pkf, double xmin, double xmax, int iparam, int niter);
+double peakfit_run(peakfit_t *pkf, int nvals, double *xvals, double *yvals);
+double peakfit_evaluate(peakfit_t *pkf);
+
+void peakfit_verbose(peakfit_t *pkf, int level);
+void peakfit_get_params(peakfit_t *pkf, int ipk, double *params, int nparams);
+void peakfit_set_params(peakfit_t *pkf, int ipk, double *params, int nparams);
+const char *peakfit_sprint_func(peakfit_t *pkf);
+
+#endif
+
diff --git a/ploidy.c b/ploidy.c
index 44dac77..160bc3e 100644
--- a/ploidy.c
+++ b/ploidy.c
@@ -33,12 +33,20 @@ struct _ploidy_t
 {
     int nsex, msex;     // number of genders, m:number of allocated elements in id2sex array
     int dflt, min, max; // ploidy: default, min and max (only explicitly listed)
+    int *sex2dflt;
     regidx_t *idx;
     void *sex2id;
     char **id2sex;
     kstring_t tmp_str;
 };
 
+typedef struct
+{
+    int sex, ploidy;
+}
+sex_ploidy_t;
+
+
 regidx_t *ploidy_regions(ploidy_t *ploidy)
 {
     return ploidy->idx;
@@ -46,16 +54,27 @@ regidx_t *ploidy_regions(ploidy_t *ploidy)
 
 int ploidy_parse(const char *line, char **chr_beg, char **chr_end, reg_t *reg, void *payload, void *usr)
 {
+    int i, ret;
     ploidy_t *ploidy = (ploidy_t*) usr;
     void *sex2id = ploidy->sex2id;
 
-    // Fill CHR,FROM,TO
-    int i, ret = regidx_parse_tab(line,chr_beg,chr_end,reg,NULL,NULL);
-    if ( ret!=0 ) return ret;
+    // Check for special case of default ploidy "* * * <sex> <ploidy>"
+    int default_ploidy_def = 0;
 
-    // Skip the fields already parsed by regidx_parse_tab
     char *ss = (char*) line;
     while ( *ss && isspace(*ss) ) ss++;
+    if ( ss[0]=='*' && (!ss[1] || isspace(ss[1])) )
+        default_ploidy_def = 1; // definition of default ploidy, chr="*"
+    else
+    {
+        // Fill CHR,FROM,TO
+        ret = regidx_parse_tab(line,chr_beg,chr_end,reg,NULL,NULL);
+        if ( ret!=0 ) return ret;
+    }
+
+    // Skip the fields already parsed by regidx_parse_tab
+    ss = (char*) line;
+    while ( *ss && isspace(*ss) ) ss++;
     for (i=0; i<3; i++)
     {
         while ( *ss && !isspace(*ss) ) ss++;
@@ -78,6 +97,8 @@ int ploidy_parse(const char *line, char **chr_beg, char **chr_end, reg_t *reg, v
         hts_expand0(char*,ploidy->nsex,ploidy->msex,ploidy->id2sex);
         ploidy->id2sex[ploidy->nsex-1] = strdup(ploidy->tmp_str.s);
         sp->sex = khash_str2int_inc(ploidy->sex2id, ploidy->id2sex[ploidy->nsex-1]);
+        ploidy->sex2dflt = (int*) realloc(ploidy->sex2dflt,sizeof(int)*ploidy->nsex);
+        ploidy->sex2dflt[ploidy->nsex-1] = ploidy->dflt;
     }
 
     ss = se;
@@ -88,6 +109,13 @@ int ploidy_parse(const char *line, char **chr_beg, char **chr_end, reg_t *reg, v
     if ( sp->ploidy < ploidy->min ) ploidy->min = sp->ploidy;
     if ( sp->ploidy > ploidy->max ) ploidy->max = sp->ploidy;
 
+    // Special case, chr="*" stands for a default value
+    if ( default_ploidy_def )
+    {
+        ploidy->sex2dflt[ploidy->nsex-1] = sp->ploidy;
+        return -1;
+    }
+
     return 0;
 }
 
@@ -141,6 +169,7 @@ void ploidy_destroy(ploidy_t *ploidy)
     if ( ploidy->idx ) regidx_destroy(ploidy->idx);
     free(ploidy->id2sex);
     free(ploidy->tmp_str.s);
+    free(ploidy->sex2dflt);
     free(ploidy);
 }
 
@@ -157,7 +186,7 @@ int ploidy_query(ploidy_t *ploidy, char *seq, int pos, int *sex2ploidy, int *min
         if ( min ) *min = ploidy->dflt;
         if ( max ) *max = ploidy->dflt;
         if ( sex2ploidy )
-            for (i=0; i<ploidy->nsex; i++) sex2ploidy[i] = ploidy->dflt;
+            for (i=0; i<ploidy->nsex; i++) sex2ploidy[i] = ploidy->sex2dflt[i];
         return 0;
     }
 
@@ -208,6 +237,8 @@ int ploidy_add_sex(ploidy_t *ploidy, const char *sex)
     ploidy->nsex++;
     hts_expand0(char*,ploidy->nsex,ploidy->msex,ploidy->id2sex);
     ploidy->id2sex[ploidy->nsex-1] = strdup(sex);
+    ploidy->sex2dflt = (int*) realloc(ploidy->sex2dflt,sizeof(int)*ploidy->nsex);
+    ploidy->sex2dflt[ploidy->nsex-1] = ploidy->dflt;
     return khash_str2int_inc(ploidy->sex2id, ploidy->id2sex[ploidy->nsex-1]);
 }
 
diff --git a/ploidy.h b/ploidy.h
index b505eb9..6deef73 100644
--- a/ploidy.h
+++ b/ploidy.h
@@ -40,13 +40,16 @@
         ploidy_destroy(pld);
 
     An example of ploidy file format follows. The coordinates are 1-based and
-    inclusive:
+    inclusive. The "*" records define the default ploidy for each sex. If not
+    present, the default_ploidy passed to ploidy_init is used instead:
         X 1 60000 M 1
         X 2699521 154931043 M 1
         Y 1 59373566 M 1
         Y 1 59373566 F 0
         MT 1 16569 M 1
         MT 1 16569 F 1
+        *  * *     M 2
+        *  * *     F 2
 */
 
 #ifndef __PLOIDY_H__
@@ -56,17 +59,10 @@
 
 typedef struct _ploidy_t ploidy_t;
 
-typedef struct
-{
-    int sex, ploidy;
-}
-sex_ploidy_t;
-
-
 /*
  *  ploidy_init()
  *  @param fname:   input file name or NULL if default ploidy from example above should be used
- *  @param dflt:    default ploidy to use for unlisted regions
+ *  @param dflt:    default ploidy to use for unlisted regions (the '* * *' records have precedence).
  *
  *  Returns new structure on success or NULL on error.
  */
diff --git a/plot-vcfstats b/plot-vcfstats
index 38d9335..5989062 100755
--- a/plot-vcfstats
+++ b/plot-vcfstats
@@ -124,7 +124,7 @@ sub parse_params
             {
                 id=>'SN',
                 header=>'SN, Summary numbers',
-                exp=>"# SN  [2]id   [3]key  [4]value"
+                exp=>"# SN\t[2]id\t[3]key\t[4]value"
             },
             {
                 id=>'TSTV',
@@ -222,6 +222,17 @@ sub parse_params
                 exp=>"# HWE\t[2]id\t[3]1st ALT allele frequency\t[4]Number of observations\t[5]25th percentile\t[6]median\t[7]75th percentile",
             },
         ],
+        SN_keys=>[
+            'number of samples:',
+            'number of records:',
+            'number of no-ALTs:',
+            'number of SNPs:',
+            'number of MNPs:',
+            'number of indels:',
+            'number of others:',
+            'number of multiallelic sites:',
+            'number of multiallelic SNP sites:',
+        ],
     };
     for my $sec (@{$$opts{sections}}) { $$opts{exp}{$$sec{id}} = $$sec{exp}; $$opts{id2sec}{$$sec{id}} = $sec; }
     while (defined(my $arg=shift(@ARGV)))
@@ -474,10 +485,24 @@ sub merge_dp
 {
     my ($a,$b) = @_;
     add_to_values($a,$b,\&cmp_num_op);
-    # recalculate fraction of GTs, cannot be simply summed
-    my $sum = 0;
-    for (my $i=0; $i<@$a; $i++) { $sum += $$a[$i][1]; }
-    for (my $i=0; $i<@$a; $i++) { $$a[$i][2] = $$a[$i][1]*100./$sum; }
+    # recalculate fraction of GTs and fraction of sites, cannot be simply summed
+    my $gsum = 0; # genotype sum
+    my $ssum = 0; # site sum
+    for (my $i=0; $i<@$a; $i++)
+    {
+        $gsum += $$a[$i][1];
+        if (@{$$a[$i]}>3) {
+            $ssum += $$a[$i][3];
+        }
+        else{
+            push @{$$a[$i]}, (0,0); # older stats files will not have last 2 columns for (number of sites, fraction of sites), so fill in as zero
+        }
+    }
+    for (my $i=0; $i<@$a; $i++)
+    {
+        $$a[$i][2] = $gsum ? $$a[$i][1]*100./$gsum : 0;
+        $$a[$i][4] = $ssum ? $$a[$i][3]*100./$ssum : 0;
+    }
 }
 
 sub merge_GCsS
@@ -852,7 +877,7 @@ sub plot_per_sample_stats
             \\tax1.set_ylabel('Ts/Tv')
             \\tax1.set_ylim(min(float(row[1]) for row in dat)-0.1,max(float(row[1]) for row in dat)+0.1)
             \\tif sample_names:
-            \\t\\t     plt.xticks([row[0] for row in dat],[row[7] for row in dat],**sample_font)
+            \\t\\t     plt.xticks([int(row[0]) for row in dat],[row[7] for row in dat],**sample_font)
             \\t\\t     plt.subplots_adjust(**sample_margins)
             \\telse:
             \\t\\t     plt.subplots_adjust(right=0.98,left=0.07,bottom=0.17)
@@ -870,7 +895,7 @@ sub plot_per_sample_stats
             \\tax1.set_ylabel('nHet(RA) / nHom(AA)')
             \\tax1.ticklabel_format(style='sci', scilimits=(0,0), axis='y')
             \\tif sample_names:
-            \\t\\t     plt.xticks([row[0] for row in dat],[row[7] for row in dat],**sample_font)
+            \\t\\t     plt.xticks([int(row[0]) for row in dat],[row[7] for row in dat],**sample_font)
             \\t\\t     plt.subplots_adjust(**sample_margins)
             \\telse:
             \\t\\t     plt.subplots_adjust(right=0.98,left=0.07,bottom=0.17)
@@ -888,7 +913,7 @@ sub plot_per_sample_stats
             \\tax1.set_ylabel('Number of SNPs')
             \\tax1.ticklabel_format(style='sci', scilimits=(0,0), axis='y')
             \\tif sample_names:
-            \\t\\t     plt.xticks([row[0] for row in dat],[row[7] for row in dat],**sample_font)
+            \\t\\t     plt.xticks([int(row[0]) for row in dat],[row[7] for row in dat],**sample_font)
             \\t\\t     plt.subplots_adjust(**sample_margins)
             \\telse:
             \\t\\t     plt.subplots_adjust(right=0.98,left=0.07,bottom=0.17)
@@ -906,7 +931,7 @@ sub plot_per_sample_stats
             \\tax1.set_ylabel('Number of indels')
             \\tax1.ticklabel_format(style='sci', scilimits=(0,0), axis='y')
             \\tif sample_names:
-            \\t\\t     plt.xticks([row[0] for row in dat],[row[7] for row in dat],**sample_font)
+            \\t\\t     plt.xticks([int(row[0]) for row in dat],[row[7] for row in dat],**sample_font)
             \\t\\t     plt.subplots_adjust(**sample_margins)
             \\telse:
             \\t\\t     plt.subplots_adjust(right=0.98,left=0.07,bottom=0.17)
@@ -924,7 +949,7 @@ sub plot_per_sample_stats
             \\tax1.set_ylabel('Number of singletons')
             \\tax1.ticklabel_format(style='sci', scilimits=(0,0), axis='y')
             \\tif sample_names:
-            \\t\\t     plt.xticks([row[0] for row in dat],[row[7] for row in dat],**sample_font)
+            \\t\\t     plt.xticks([int(row[0]) for row in dat],[row[7] for row in dat],**sample_font)
             \\t\\t     plt.subplots_adjust(**sample_margins)
             \\telse:
             \\t\\t     plt.subplots_adjust(right=0.98,left=0.07,bottom=0.17)
@@ -942,7 +967,7 @@ sub plot_per_sample_stats
             \\tax1.set_ylabel('Average depth')
             \\tax1.ticklabel_format(style='sci', scilimits=(0,0), axis='y')
             \\tif sample_names:
-            \\t\\t     plt.xticks([row[0] for row in dat],[row[7] for row in dat],**sample_font)
+            \\t\\t     plt.xticks([int(row[0]) for row in dat],[row[7] for row in dat],**sample_font)
             \\t\\t     plt.subplots_adjust(**sample_margins)
             \\telse:
             \\t\\t     plt.subplots_adjust(right=0.98,left=0.07,bottom=0.17)
@@ -1281,7 +1306,7 @@ sub plot_tstv_by_QUAL
             \\tfor row in reader:
             \\t\\tif row[0][0] != '#': dat.append([float(x) for x in row])
 
-            if plot_tstv_by_qual:
+            if plot_tstv_by_qual and len(dat)>2:
             \\tfig = plt.figure(figsize=($$opts{img_width},$$opts{img_height}))
             \\tax1 = fig.add_subplot(111)
             \\tax1.plot([row[1] for row in dat], [row[2] for row in dat], '^-', ms=3, mec='$$opts{id2col}[$id]', color='$$opts{id2col}[$id]')
@@ -1444,7 +1469,7 @@ sub plot_concordance_by_sample
             \\tax1.set_ylabel('Non-ref discordance')
             \\tax1.set_ylim(0,)
             \\tif sample_names:
-            \\t\\t     plt.xticks([row[0] for row in dat],[row[2] for row in dat],**sample_font)
+            \\t\\t     plt.xticks([int(row[0]) for row in dat],[row[2] for row in dat],**sample_font)
             \\t\\t     plt.subplots_adjust(**sample_margins)
             \\telse:
             \\t\\t     plt.subplots_adjust(right=0.98,left=0.07,bottom=0.17)
@@ -1599,10 +1624,8 @@ sub plot_overlap_by_AF_col
 
 
     ";
-
 }
 
-
 sub plot_indel_distribution
 {
     my ($opts,$id) = @_;
@@ -1755,6 +1778,7 @@ sub fmt_slide3v
             \\hslide{$title}{$slide}
         ];
 }
+
 sub fmt_slide3h
 {
     my ($opts, $image, $title) = @_;
@@ -2083,7 +2107,6 @@ sub create_pdf
     print STDERR "Finished: $pdf_file\n" unless !$$opts{verbose};
 }
 
-
 sub merge_vcfstats
 {
     my ($opts) = @_;
@@ -2117,8 +2140,9 @@ sub merge_vcfstats
             for my $id (keys %{$$opts{dat}})
             {
                 if ( exists($$opts{exp}{$id}) ) { next; }
-                for my $key (keys %{$$opts{dat}{$id}})
+                for my $key (@{$$opts{SN_keys}})
                 {
+                    next unless exists $$opts{dat}{$id}{$key};
                     print $fh "SN\t$id\t$key\t$$opts{dat}{$id}{$key}\n";
                 }
             }
diff --git a/plugins/color-chrs.c b/plugins/color-chrs.c
new file mode 100644
index 0000000..6a9175e
--- /dev/null
+++ b/plugins/color-chrs.c
@@ -0,0 +1,559 @@
+/* The MIT License
+
+   Copyright (c) 2015 Genome Research Ltd.
+
+   Author: Petr Danecek <pd3 at sanger.ac.uk>
+   
+   Permission is hereby granted, free of charge, to any person obtaining a copy
+   of this software and associated documentation files (the "Software"), to deal
+   in the Software without restriction, including without limitation the rights
+   to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+   copies of the Software, and to permit persons to whom the Software is
+   furnished to do so, subject to the following conditions:
+   
+   The above copyright notice and this permission notice shall be included in
+   all copies or substantial portions of the Software.
+   
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+   IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+   FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+   AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+   LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+   OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+   THE SOFTWARE.
+
+ */
+
+/*
+    Trio haplotypes: mother (A,B), father (C,D), child (E,F)
+    Modeling the following states:
+        01|23|02 
+        01|23|03
+        01|23|12
+        01|23|13
+        01|23|20
+        01|23|30
+        01|23|21
+        01|23|31
+    with the likelihoods of two haplotypes A,B segments sharing an allele:
+        P(01|A==B)  .. e (P of error)
+        P(00|A==B)  .. 1-e
+    and
+        P(ab,cd,ef|E=A,F=C) = P(ea|E=A)*P(fc|F=C)
+
+
+    Unrelated samples: (A,B) and (C,D)
+    Modeling the states:
+        xxxx .. A!=C,A!=D,B!=C,B!=D
+        0x0x .. A=C,B!=D
+        0xx0 .. A=D,B!=C
+        x00x .. B=C,A!=D
+        x0x0 .. B=D,A!=C
+        0101 .. A=C,B=D
+        0110 .. A=D,B=C
+    with the likelihoods
+        P(01|A!=B)  .. f*(1-f)
+        P(00|A!=B)  .. (1-f)*(1-f)
+        P(11|A!=B)  .. f*f
+
+    Assuming 2x30 crossovers, P=2e-8.
+ */
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <getopt.h>
+#include <math.h>
+#include <htslib/hts.h>
+#include <htslib/vcf.h>
+#include <errno.h>
+#include "bcftools.h"
+#include "HMM.h"
+
+#define C_TRIO 1
+#define C_UNRL 2
+
+// states for unrelated samples
+#define UNRL_xxxx  0
+#define UNRL_0x0x  1
+#define UNRL_0xx0  2
+#define UNRL_x00x  3
+#define UNRL_x0x0  4
+#define UNRL_0101  5
+#define UNRL_0110  6
+
+// trio states
+#define TRIO_AC 0
+#define TRIO_AD 1
+#define TRIO_BC 2
+#define TRIO_BD 3
+#define TRIO_CA 4
+#define TRIO_DA 5
+#define TRIO_CB 6
+#define TRIO_DB 7
+
+typedef struct _args_t
+{
+    bcf_hdr_t *hdr;
+    hmm_t *hmm;
+    double *eprob, *tprob, pij, pgt_err;
+    uint32_t *sites;
+    int32_t *gt_arr;
+    int nsites, msites, ngt_arr, prev_rid;
+    int mode, nstates, nhet_father, nhet_mother;
+    int imother,ifather,ichild, isample,jsample;
+    void (*set_observed_prob) (bcf1_t *rec);
+    char *prefix;
+    FILE *fp;
+}
+args_t;
+
+static args_t args;
+
+#define SW_MOTHER 1
+#define SW_FATHER 2
+static int hap_switch[8][8];
+
+static void set_observed_prob_trio(bcf1_t *rec);
+static void set_observed_prob_unrelated(bcf1_t *rec);
+static void init_hmm_trio(args_t *args);
+static void init_hmm_unrelated(args_t *args);
+
+
+const char *about(void)
+{
+    return "Color shared chromosomal segments, requires phased GTs.\n";
+}
+
+const char *usage(void)
+{
+    return 
+        "\n"
+        "About: Color shared chromosomal segments, requires phased GTs.\n"
+        "Usage: bcftools +color-chrs [General Options] -- [Plugin Options]\n"
+        "Options:\n"
+        "   run \"bcftools plugin\" for a list of common options\n"
+        "\n"
+        "Plugin options:\n"
+        "   -p, --prefix <path>     output files prefix\n"
+        "   -t, --trio <m,f,c>      names of mother, father and the child\n"
+        "   -u, --unrelated <a,b>   names of two unrelated samples\n"
+        "\n"
+        "Example:\n"
+        "   bcftools +color-chrs in.vcf --\n"
+        "\n";
+}
+
+int init(int argc, char **argv, bcf_hdr_t *in, bcf_hdr_t *out)
+{
+    char *trio_samples = NULL, *unrelated_samples = NULL;
+    memset(&args,0,sizeof(args_t));
+    args.prev_rid = -1;
+    args.hdr = in;
+    args.pij = 2e-8;
+    args.pgt_err = 1e-9;
+
+    static struct option loptions[] =
+    {
+        {"prefix",1,0,'p'},
+        {"trio",1,0,'t'},
+        {"unrelated",1,0,'u'},
+        {0,0,0,0}
+    };
+    char c;
+    while ((c = getopt_long(argc, argv, "?ht:u:p:",loptions,NULL)) >= 0)
+    {
+        switch (c) 
+        {
+            case 'p': args.prefix = optarg; break;
+            case 't': trio_samples = optarg; break;
+            case 'u': unrelated_samples = optarg; break;
+            case 'h':
+            case '?':
+            default: error("%s", usage()); break;
+        }
+    }
+    if ( optind != argc ) error(usage());
+    if ( trio_samples && unrelated_samples ) error("Expected only one of the -t/-u options\n");
+    if ( !trio_samples && !unrelated_samples ) error("Expected one of the -t/-u options\n");
+    if ( !args.prefix ) error("Expected the -p option\n");
+
+    int ret = bcf_hdr_set_samples(args.hdr, trio_samples ? trio_samples : unrelated_samples, 0);
+    if ( ret<0 ) error("Could not parse samples: %s\n", trio_samples ? trio_samples : unrelated_samples);
+    else if ( ret>0 ) error("%d-th sample not found: %s\n", ret,trio_samples ? trio_samples : unrelated_samples);
+
+    if ( trio_samples )
+    {
+        int i,n = 0;
+        char **list = hts_readlist(trio_samples, 0, &n);
+        if ( n!=3 ) error("Expected three sample names with -t\n");
+        args.imother = bcf_hdr_id2int(args.hdr, BCF_DT_SAMPLE, list[0]);
+        args.ifather = bcf_hdr_id2int(args.hdr, BCF_DT_SAMPLE, list[1]);
+        args.ichild  = bcf_hdr_id2int(args.hdr, BCF_DT_SAMPLE, list[2]);
+        for (i=0; i<n; i++) free(list[i]);
+        free(list);
+        args.set_observed_prob = set_observed_prob_trio;
+        args.mode = C_TRIO;
+        init_hmm_trio(&args);
+    }
+    else
+    {
+        int i,n = 0;
+        char **list = hts_readlist(unrelated_samples, 0, &n);
+        if ( n!=2 ) error("Expected two sample names with -u\n");
+        args.isample = bcf_hdr_id2int(args.hdr, BCF_DT_SAMPLE, list[0]);
+        args.jsample = bcf_hdr_id2int(args.hdr, BCF_DT_SAMPLE, list[1]);
+        for (i=0; i<n; i++) free(list[i]);
+        free(list);
+        args.set_observed_prob = set_observed_prob_unrelated;
+        args.mode = C_UNRL;
+        init_hmm_unrelated(&args);
+    }
+    return 1;
+}
+
+static void init_hmm_trio(args_t *args)
+{
+    int i,j;
+    args->nstates = 8;
+    args->tprob   = (double*) malloc(sizeof(double)*args->nstates*args->nstates);
+
+    for (i=0; i<args->nstates; i++)
+        for (j=0; j<args->nstates; j++) hap_switch[i][j] = 0;
+
+    hap_switch[TRIO_AD][TRIO_AC] = SW_FATHER;
+    hap_switch[TRIO_BC][TRIO_AC] = SW_MOTHER;
+    hap_switch[TRIO_BD][TRIO_AC] = SW_MOTHER | SW_FATHER;
+    hap_switch[TRIO_AC][TRIO_AD] = SW_FATHER;
+    hap_switch[TRIO_BC][TRIO_AD] = SW_MOTHER | SW_FATHER;
+    hap_switch[TRIO_BD][TRIO_AD] = SW_MOTHER;
+    hap_switch[TRIO_AC][TRIO_BC] = SW_MOTHER;
+    hap_switch[TRIO_AD][TRIO_BC] = SW_MOTHER | SW_FATHER;
+    hap_switch[TRIO_BD][TRIO_BC] = SW_FATHER;
+    hap_switch[TRIO_AC][TRIO_BD] = SW_MOTHER | SW_FATHER;
+    hap_switch[TRIO_AD][TRIO_BD] = SW_MOTHER;
+    hap_switch[TRIO_BC][TRIO_BD] = SW_FATHER;
+
+    hap_switch[TRIO_DA][TRIO_CA] = SW_FATHER;
+    hap_switch[TRIO_CB][TRIO_CA] = SW_MOTHER;
+    hap_switch[TRIO_DB][TRIO_CA] = SW_MOTHER | SW_FATHER;
+    hap_switch[TRIO_CA][TRIO_DA] = SW_FATHER;
+    hap_switch[TRIO_CB][TRIO_DA] = SW_MOTHER | SW_FATHER;
+    hap_switch[TRIO_DB][TRIO_DA] = SW_MOTHER;
+    hap_switch[TRIO_CA][TRIO_CB] = SW_MOTHER;
+    hap_switch[TRIO_DA][TRIO_CB] = SW_MOTHER | SW_FATHER;
+    hap_switch[TRIO_DB][TRIO_CB] = SW_FATHER;
+    hap_switch[TRIO_CA][TRIO_DB] = SW_MOTHER | SW_FATHER;
+    hap_switch[TRIO_DA][TRIO_DB] = SW_MOTHER;
+    hap_switch[TRIO_CB][TRIO_DB] = SW_FATHER;
+
+    for (i=0; i<args->nstates; i++)
+    {
+        for (j=0; j<args->nstates; j++)
+        {
+            if ( !hap_switch[i][j] ) MAT(args->tprob,args->nstates,i,j) = 0;
+            else
+            {
+                MAT(args->tprob,args->nstates,i,j) = 1;
+                if ( hap_switch[i][j] & SW_MOTHER ) MAT(args->tprob,args->nstates,i,j) *= args->pij;
+                if ( hap_switch[i][j] & SW_FATHER ) MAT(args->tprob,args->nstates,i,j) *= args->pij;
+            }
+        }
+    }
+    for (i=0; i<args->nstates; i++)
+    {
+        double sum = 0;
+        for (j=0; j<args->nstates; j++)
+        {
+            if ( i!=j ) sum += MAT(args->tprob,args->nstates,i,j);
+        }
+        MAT(args->tprob,args->nstates,i,i) = 1 - sum;
+    }
+
+    #if 0
+    for (i=0; i<args->nstates; i++)
+    {
+        for (j=0; j<args->nstates; j++)
+            fprintf(stderr,"\t%d",hap_switch[j][i]);
+        fprintf(stderr,"\n");
+    }
+    for (i=0; i<args->nstates; i++)
+    {
+        for (j=0; j<args->nstates; j++)
+            fprintf(stderr,"\t%e",MAT(args->tprob,args->nstates,j,i));
+        fprintf(stderr,"\n");
+    }
+    #endif
+
+    args->hmm = hmm_init(args->nstates, args->tprob, 10000);
+}
+static void init_hmm_unrelated(args_t *args)
+{
+    int i,j;
+    args->nstates = 7;
+    args->tprob   = (double*) malloc(sizeof(double)*args->nstates*args->nstates);
+
+    for (i=0; i<args->nstates; i++)
+    {
+        for (j=0; j<args->nstates; j++)
+            MAT(args->tprob,args->nstates,i,j) = args->pij;
+    }
+    MAT(args->tprob,args->nstates,UNRL_0101,UNRL_xxxx) = args->pij*args->pij;
+    MAT(args->tprob,args->nstates,UNRL_0110,UNRL_xxxx) = args->pij*args->pij;
+    MAT(args->tprob,args->nstates,UNRL_x0x0,UNRL_0x0x) = args->pij*args->pij;
+    MAT(args->tprob,args->nstates,UNRL_0110,UNRL_0x0x) = args->pij*args->pij;
+    MAT(args->tprob,args->nstates,UNRL_x00x,UNRL_0xx0) = args->pij*args->pij;
+    MAT(args->tprob,args->nstates,UNRL_0101,UNRL_0xx0) = args->pij*args->pij;
+    MAT(args->tprob,args->nstates,UNRL_0101,UNRL_x00x) = args->pij*args->pij;
+    MAT(args->tprob,args->nstates,UNRL_0110,UNRL_x0x0) = args->pij*args->pij;
+    MAT(args->tprob,args->nstates,UNRL_0110,UNRL_0101) = args->pij*args->pij;
+
+    for (i=0; i<args->nstates; i++)
+    {
+        for (j=i+1; j<args->nstates; j++)
+            MAT(args->tprob,args->nstates,i,j) = MAT(args->tprob,args->nstates,j,i);
+    }
+    for (i=0; i<args->nstates; i++)
+    {
+        double sum = 0;
+        for (j=0; j<args->nstates; j++)
+            if ( i!=j ) sum += MAT(args->tprob,args->nstates,i,j);
+        MAT(args->tprob,args->nstates,i,i) = 1 - sum;
+    }
+
+    #if 0
+    for (i=0; i<args->nstates; i++)
+    {
+        for (j=0; j<args->nstates; j++)
+            fprintf(stderr,"\t%e",MAT(args->tprob,args->nstates,j,i));
+        fprintf(stderr,"\n");
+    }
+    #endif
+
+    args->hmm = hmm_init(args->nstates, args->tprob, 10000);
+}
+static inline double prob_shared(float af, int a, int b)
+{
+    return a==b ? 1-args.pgt_err : args.pgt_err;
+}
+static inline double prob_not_shared(float af, int a, int b)
+{
+    if ( a!=b ) return af*(1-af);
+    else if ( a==0 ) return (1-af)*(1-af);
+    else return af*af;
+}
+static void set_observed_prob_unrelated(bcf1_t *rec)
+{
+    float af = 0.5;  // alternate allele frequency
+
+    int ngt = bcf_get_genotypes(args.hdr, rec, &args.gt_arr, &args.ngt_arr);
+    if ( ngt<0 ) return;
+    if ( ngt!=4 ) return;   // chrX
+
+    int32_t a,b,c,d;
+    a = args.gt_arr[2*args.isample];
+    b = args.gt_arr[2*args.isample+1];
+    c = args.gt_arr[2*args.jsample];
+    d = args.gt_arr[2*args.jsample+1];
+    if ( bcf_gt_is_missing(a) || bcf_gt_is_missing(b) ) return;
+    if ( bcf_gt_is_missing(c) || bcf_gt_is_missing(d) ) return;
+    if ( !bcf_gt_is_phased(a) && !bcf_gt_is_phased(b) ) return; // only the second allele should be set when phased
+    if ( !bcf_gt_is_phased(c) && !bcf_gt_is_phased(d) ) return;
+    a = bcf_gt_allele(a);
+    b = bcf_gt_allele(b);
+    c = bcf_gt_allele(c);
+    d = bcf_gt_allele(d);
+
+    int m = args.msites;
+    args.nsites++;
+    hts_expand(uint32_t,args.nsites,args.msites,args.sites);
+    if ( m!=args.msites ) args.eprob = (double*) realloc(args.eprob, sizeof(double)*args.msites*args.nstates);
+
+    args.sites[args.nsites-1] = rec->pos;
+    double *prob = args.eprob + args.nstates*(args.nsites-1);
+    prob[UNRL_xxxx] = prob_not_shared(af,a,c) * prob_not_shared(af,a,d) * prob_not_shared(af,b,c) * prob_not_shared(af,b,d);
+    prob[UNRL_0x0x] = prob_shared(af,a,c) * prob_not_shared(af,b,d);
+    prob[UNRL_0xx0] = prob_shared(af,a,d) * prob_not_shared(af,b,c);
+    prob[UNRL_x00x] = prob_shared(af,b,c) * prob_not_shared(af,a,d);
+    prob[UNRL_x0x0] = prob_shared(af,b,d) * prob_not_shared(af,a,c);
+    prob[UNRL_0101] = prob_shared(af,a,c) * prob_shared(af,b,d);
+    prob[UNRL_0110] = prob_shared(af,a,d) * prob_shared(af,b,c);
+
+#if 0
+    static int x = 0;
+    if ( !x++)
+    {
+        printf("p(0==0) .. %f\n", prob_shared(af,0,0));
+        printf("p(0!=0) .. %f\n", prob_not_shared(af,0,0));
+        printf("p(0==1) .. %f\n", prob_shared(af,0,1));
+        printf("p(0!=1) .. %f\n", prob_not_shared(af,0,1));
+    }
+    printf("%d|%d %d|%d  x:%f 11:%f 12:%f 21:%f 22:%f 11,22:%f 12,21:%f  %d\n", a,b,c,d,
+            prob[UNRL_xxxx], prob[UNRL_0x0x], prob[UNRL_0xx0], prob[UNRL_x00x], prob[UNRL_x0x0], prob[UNRL_0101], prob[UNRL_0110], rec->pos+1);
+#endif
+}
+static void set_observed_prob_trio(bcf1_t *rec)
+{
+    int ngt = bcf_get_genotypes(args.hdr, rec, &args.gt_arr, &args.ngt_arr);
+    if ( ngt<0 ) return;
+    if ( ngt!=6 ) return;   // chrX
+
+    int32_t a,b,c,d,e,f;
+    a = args.gt_arr[2*args.imother];
+    b = args.gt_arr[2*args.imother+1];
+    c = args.gt_arr[2*args.ifather];
+    d = args.gt_arr[2*args.ifather+1];
+    e = args.gt_arr[2*args.ichild];
+    f = args.gt_arr[2*args.ichild+1];
+    if ( bcf_gt_is_missing(a) || bcf_gt_is_missing(b) ) return;
+    if ( bcf_gt_is_missing(c) || bcf_gt_is_missing(d) ) return;
+    if ( bcf_gt_is_missing(e) || bcf_gt_is_missing(f) ) return;
+    if ( !bcf_gt_is_phased(a) && !bcf_gt_is_phased(b) ) return; // only the second allele should be set when phased
+    if ( !bcf_gt_is_phased(c) && !bcf_gt_is_phased(d) ) return;
+    if ( !bcf_gt_is_phased(e) && !bcf_gt_is_phased(f) ) return;
+    a = bcf_gt_allele(a);
+    b = bcf_gt_allele(b);
+    c = bcf_gt_allele(c);
+    d = bcf_gt_allele(d);
+    e = bcf_gt_allele(e);
+    f = bcf_gt_allele(f);
+
+    int mother = (1<<a) | (1<<b);
+    int father = (1<<c) | (1<<d);
+    int child  = (1<<e) | (1<<f);
+    if ( !(mother&child) || !(father&child) )  return;      // Mendelian-inconsistent site, skip
+
+    if ( a!=b ) args.nhet_mother++;
+    if ( c!=d ) args.nhet_father++;
+
+    int m = args.msites;
+    args.nsites++;
+    hts_expand(uint32_t,args.nsites,args.msites,args.sites);
+    if ( m!=args.msites ) args.eprob = (double*) realloc(args.eprob, sizeof(double)*args.msites*args.nstates);
+
+    args.sites[args.nsites-1] = rec->pos;
+    double *prob = args.eprob + args.nstates*(args.nsites-1);
+    prob[TRIO_AC] = prob_shared(0,e,a) * prob_shared(0,f,c);
+    prob[TRIO_AD] = prob_shared(0,e,a) * prob_shared(0,f,d);
+    prob[TRIO_BC] = prob_shared(0,e,b) * prob_shared(0,f,c);
+    prob[TRIO_BD] = prob_shared(0,e,b) * prob_shared(0,f,d);
+    prob[TRIO_CA] = prob_shared(0,e,c) * prob_shared(0,f,a);
+    prob[TRIO_DA] = prob_shared(0,e,d) * prob_shared(0,f,a);
+    prob[TRIO_CB] = prob_shared(0,e,c) * prob_shared(0,f,b);
+    prob[TRIO_DB] = prob_shared(0,e,d) * prob_shared(0,f,b);
+}
+
+void flush_viterbi(args_t *args)
+{
+    const char *s1, *s2, *s3 = NULL;
+    if ( args->mode==C_UNRL )
+    {
+        s1 = bcf_hdr_int2id(args->hdr,BCF_DT_SAMPLE,args->isample);
+        s2 = bcf_hdr_int2id(args->hdr,BCF_DT_SAMPLE,args->jsample);
+    }
+    else if ( args->mode==C_TRIO )
+    {
+        s1 = bcf_hdr_int2id(args->hdr,BCF_DT_SAMPLE,args->imother);
+        s3 = bcf_hdr_int2id(args->hdr,BCF_DT_SAMPLE,args->ifather);
+        s2 = bcf_hdr_int2id(args->hdr,BCF_DT_SAMPLE,args->ichild);
+    }
+
+    if ( !args->fp )
+    {
+        kstring_t str = {0,0,0};
+        kputs(args->prefix, &str);
+        kputs(".dat", &str);
+        args->fp = fopen(str.s,"w");
+        if ( !args->fp ) error("%s: %s\n", str.s,strerror(errno));
+        free(str.s);
+        fprintf(args->fp,"# SG, shared segment\t[2]Chromosome\t[3]Start\t[4]End\t[5]%s:1\t[6]%s:2\n",s2,s2);
+        fprintf(args->fp,"# SW, number of switches\t[3]Sample\t[4]Chromosome\t[5]nHets\t[5]nSwitches\t[6]switch rate\n");
+    }
+
+    hmm_run_viterbi(args->hmm,args->nsites,args->eprob,args->sites);
+    uint8_t *vpath = hmm_get_viterbi_path(args->hmm);
+    int i, iprev = -1, prev_state = -1, nstates = hmm_get_nstates(args->hmm);
+    int nswitch_mother = 0, nswitch_father = 0;
+    for (i=0; i<args->nsites; i++)
+    {
+        int state = vpath[i*nstates];
+        if ( state!=prev_state || i+1==args->nsites )
+        {
+            uint32_t start = iprev>=0 ? args->sites[iprev]+1 : 1, end = i>0 ? args->sites[i-1] : 1;
+            const char *chr = bcf_hdr_id2name(args->hdr,args->prev_rid);
+            if ( args->mode==C_UNRL )
+            {
+                switch (prev_state)
+                {
+                    case UNRL_0x0x:
+                        fprintf(args->fp,"SG\t%s\t%d\t%d\t%s:1\t-\n", chr,start,end,s1); break;
+                    case UNRL_0xx0:
+                        fprintf(args->fp,"SG\t%s\t%d\t%d\t-\t%s:1\n", chr,start,end,s1); break;
+                    case UNRL_x00x:
+                        fprintf(args->fp,"SG\t%s\t%d\t%d\t%s:2\t-\n", chr,start,end,s1); break;
+                    case UNRL_x0x0:
+                        fprintf(args->fp,"SG\t%s\t%d\t%d\t-\t%s:2\n", chr,start,end,s1); break;
+                    case UNRL_0101:
+                        fprintf(args->fp,"SG\t%s\t%d\t%d\t%s:1\t%s:2\n", chr,start,end,s1,s1); break;
+                    case UNRL_0110:
+                        fprintf(args->fp,"SG\t%s\t%d\t%d\t%s:2\t%s:1\n", chr,start,end,s1,s1); break;
+                }
+            }
+            else if ( args->mode==C_TRIO )
+            {
+                switch (prev_state)
+                {
+                    case TRIO_AC:
+                        fprintf(args->fp,"SG\t%s\t%d\t%d\t%s:1\t%s:1\n", chr,start,end,s1,s3); break;
+                    case TRIO_AD:
+                        fprintf(args->fp,"SG\t%s\t%d\t%d\t%s:1\t%s:2\n", chr,start,end,s1,s3); break;
+                    case TRIO_BC:
+                        fprintf(args->fp,"SG\t%s\t%d\t%d\t%s:2\t%s:1\n", chr,start,end,s1,s3); break;
+                    case TRIO_BD:
+                        fprintf(args->fp,"SG\t%s\t%d\t%d\t%s:2\t%s:2\n", chr,start,end,s1,s3); break;
+                    case TRIO_CA:
+                        fprintf(args->fp,"SG\t%s\t%d\t%d\t%s:1\t%s:1\n", chr,start,end,s3,s1); break;
+                    case TRIO_DA:
+                        fprintf(args->fp,"SG\t%s\t%d\t%d\t%s:2\t%s:1\n", chr,start,end,s3,s1); break;
+                    case TRIO_CB:
+                        fprintf(args->fp,"SG\t%s\t%d\t%d\t%s:1\t%s:2\n", chr,start,end,s3,s1); break;
+                    case TRIO_DB:
+                        fprintf(args->fp,"SG\t%s\t%d\t%d\t%s:2\t%s:2\n", chr,start,end,s3,s1); break;
+                }
+                if ( hap_switch[state][prev_state] & SW_MOTHER ) nswitch_mother++;
+                if ( hap_switch[state][prev_state] & SW_FATHER ) nswitch_father++;
+            }
+            iprev = i-1;
+        }
+        prev_state = state;
+    }
+    float mrate = args->nhet_mother>1 ? (float)nswitch_mother/(args->nhet_mother-1) : 0;
+    float frate = args->nhet_father>1 ? (float)nswitch_father/(args->nhet_father-1) : 0;
+    fprintf(args->fp,"SW\t%s\t%s\t%d\t%d\t%f\n", s1,bcf_hdr_id2name(args->hdr,args->prev_rid),args->nhet_mother,nswitch_mother,mrate);
+    fprintf(args->fp,"SW\t%s\t%s\t%d\t%d\t%f\n", s3,bcf_hdr_id2name(args->hdr,args->prev_rid),args->nhet_father,nswitch_father,frate);
+    args->nsites = 0;
+    args->nhet_father = args->nhet_mother = 0;
+}
+    
+bcf1_t *process(bcf1_t *rec)
+{
+    if ( args.prev_rid==-1 ) args.prev_rid = rec->rid;
+    if ( args.prev_rid!=rec->rid ) flush_viterbi(&args);
+    args.prev_rid = rec->rid;
+    args.set_observed_prob(rec);
+    return NULL;
+}
+
+void destroy(void)
+{
+    flush_viterbi(&args);
+    fclose(args.fp);
+
+    free(args.gt_arr);
+    free(args.tprob);
+    free(args.sites);
+    free(args.eprob);
+    hmm_destroy(args.hmm);
+}
+
+
+
diff --git a/plugins/color-chrs.mk b/plugins/color-chrs.mk
new file mode 100644
index 0000000..506b99d
--- /dev/null
+++ b/plugins/color-chrs.mk
@@ -0,0 +1,2 @@
+plugins/color-chrs.so: plugins/color-chrs.c version.h version.c HMM.h HMM.c
+	$(CC) $(PLUGIN_FLAGS) $(CFLAGS) $(EXTRA_CPPFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $@ HMM.c version.c $< $(LIBS)
diff --git a/plugins/color-chrs.pl b/plugins/color-chrs.pl
new file mode 100755
index 0000000..4afb9c7
--- /dev/null
+++ b/plugins/color-chrs.pl
@@ -0,0 +1,528 @@
+#!/usr/bin/env perl
+#
+#   Copyright (C) 2015 Genome Research Ltd.
+#
+#   Author: Petr Danecek <pd3 at sanger.ac.uk>
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+# THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+# DEALINGS IN THE SOFTWARE.
+
+use strict;
+use warnings;
+use Carp;
+
+my $opts = parse_params();
+chr_dims($opts);
+for my $file (@{$$opts{files}})
+{
+    read_dat($opts,$file);
+}
+merge_regs($opts);
+plot($opts);
+
+exit;
+
+#--------------------------------
+
+sub error
+{
+    my (@msg) = @_;
+    if ( scalar @msg ) { confess @msg; }
+    print 
+        "About: Plot output of \"bcftools +color-chrs\"\n",
+        "Usage: color-chrs.pl [OPTIONS] output.dat\n",
+        "Options:\n",
+        "   -c, --colors <file>         File with list of \"chr hap color\".\n",
+        "   -p, --prefix <name>         Prefix of output files.\n",
+        "   -h, -?, --help              This help message.\n",
+        "\n";
+    exit -1;
+}
+
+sub parse_params
+{
+    my $opts =
+    {
+        #colors => ['red','green','blue','yellow'],
+        colors => ['#ff0000','#008000','#0000ff','#ffff00'],
+        height => 350,
+        pad    => 10,
+        dimL   => 300,     # arm length
+        dimD   => 10,      # arm width
+        dimE   => 7,       # arm pad
+        dimB   => 5,       # arm end curve
+    };
+    $$opts{chr_width} = 2*$$opts{pad} + 2*$$opts{dimD} + $$opts{dimE};
+    $$opts{width} = $$opts{chr_width}*23;
+    while (defined(my $arg=shift(@ARGV)))
+    {
+        if ( -e $arg ) { push @{$$opts{files}},$arg; next }
+        if ( $arg eq '-p' || $arg eq '--prefix' ) { $$opts{prefix}=shift(@ARGV); next }
+        if ( $arg eq '-c' || $arg eq '--colors' ) { read_colors($opts,shift(@ARGV)); next; }
+        if ( $arg eq '-?' || $arg eq '-h' || $arg eq '--help' ) { error(); }
+        error("Unknown parameter \"$arg\". Run -h for help.\n");
+    }
+    if ( !exists($$opts{files}) ) { error("No files given?\n") }
+    if ( !exists($$opts{prefix}) ) { error("Expected -p option\n") }
+    return $opts;
+}
+
+sub read_colors
+{
+    my ($opts,$fname) = @_;
+    open(my $fh,'<',$fname) or error("$fname: $!");
+    while (my $line=<$fh>)
+    {
+        if ( $line=~/^\s*$/ ) { next; }
+        $line =~ s/^\s*//;
+        $line =~ s/\s*$//;
+        my ($chr,$hap,$col) = split(/\s+/,$line);
+        $$opts{hap_cols}{$chr}{$hap} = $col;
+    }
+    close($fh);
+}
+
+sub plot
+{
+    my ($opts) = @_;
+
+    my $width  = $$opts{width};
+    my $height = $$opts{height};
+    my $pad    = $$opts{pad};
+
+    my $svg = $$opts{svg} = [];
+    push @$svg, q[<?xml version="1.0" encoding="UTF-8" standalone="yes"?>];
+    push @$svg, q[<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.0//EN" "http://www.w3.org/TR/2001/REC-SVG-20010904/DTD/svg10.dtd">];
+    push @$svg, qq[<svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" height="100%" viewBox="0 0 $width $height" width="100%">];
+
+    my $xpos = $pad;
+    for my $chr (qw(1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X))
+    {
+        draw_chr($opts,$chr,$xpos,$pad);
+        $xpos += $$opts{chr_width};
+    }
+    $xpos = $pad + 10*$$opts{chr_width};
+    for my $sample (keys %{$$opts{samples}})
+    {
+        $$opts{chrs}{$sample} = { len=>59e6, acen=>[24e6,26e6,28e6] };
+        my $chr  = $$opts{chrs}{$sample};
+        my $len1 = $$opts{dimL}*$$chr{acen}[0]/$$opts{max_chr_len};
+        my $len2 = $$opts{dimL}*$$chr{acen}[2]/$$opts{max_chr_len};
+        my $len3 = $$opts{dimL}*$$chr{len}/$$opts{max_chr_len};
+        if ( exists($$opts{samples}{$sample}{1}) )
+        {
+            my $col = $$opts{samples}{$sample}{1};
+            $$chr{px1} = [[0,$len1,{$col=>1.0}],[$len2,$len3,{$col=>1.0}]]; 
+        }
+        if ( exists($$opts{samples}{$sample}{2}) )
+        {
+            my $col = $$opts{samples}{$sample}{2};
+            $$chr{px2} = [[0,$len1,{$col=>1.0}],[$len2,$len3,{$col=>1.0}]]; 
+        }
+        my $ypos = $$opts{dimL} - $len3 + $pad;
+        draw_chr($opts,$sample,$xpos,$ypos);
+        $xpos += 2*$$opts{chr_width};
+    }
+
+    push @$svg, q[</svg>];
+    open(my $fh,'>',"$$opts{prefix}.svg");
+    print $fh join("\n",@$svg);
+    close($fh);
+}
+
+sub draw_chr
+{
+    my ($opts,$chr_name,$xpos,$ypos) = @_;
+
+    my $svg = $$opts{svg};
+    my $chr = $$opts{chrs}{$chr_name};
+    my $dimL  = $$opts{dimL};
+    my $dimC  = $dimL*($$chr{acen}[2]-$$chr{acen}[0])/$$opts{max_chr_len};
+    my $dimL1 = $dimL*$$chr{acen}[0]/$$opts{max_chr_len};
+    my $dimL2 = $dimL*($$chr{len} - $$chr{acen}[2])/$$opts{max_chr_len};
+    my $dimD  = $$opts{dimD};   # arm width
+    my $dimB  = $$opts{dimB};
+    my $dimE  = $$opts{dimE};   # the gap width between arms
+    my $dimE05 = $dimE*0.5;
+    my $dimD05 = $dimD*0.5;
+    my $dimB05 = $dimB*0.5;
+    my $dimC05 = 0.5*$dimC;
+
+    my $xtext = $xpos + $dimD + $dimE*0.5;
+    my $ytext = $ypos;
+    push @$svg, qq[<text text-anchor="middle" x="$xtext" y="$ytext">$chr_name</text>\n];
+
+    $ypos += $$opts{pad};
+
+    push @$svg, qq[
+        <path d="M$xpos $ypos
+                 l0 $dimL1
+                 q$dimB $dimC05 0 $dimC
+                 l0 $dimL2
+                 q$dimD05 $dimB $dimD 0
+                 l0 -$dimL2
+                 q$dimE05 -$dimB $dimE 0 ];
+
+    # bottom part of the right arm 
+    push @$svg, qq[
+                 l0 $dimL2
+                 q$dimD05 $dimB $dimD 0
+                 l0 -$dimL2
+                 q-$dimB -$dimC05 0 -$dimC
+                 l0 -$dimL1
+                 q-$dimD05 -$dimB -$dimD 0
+                 l0 $dimL1
+                 q-$dimE05 $dimB -$dimE 0
+                 l0 -$dimL1
+                 q-$dimD05 -$dimB -$dimD 0
+                 "
+              style="stroke:#333; fill:#aaa;"/> ];
+
+    if ( $$chr{px1} ) { draw_regs($opts,$chr_name,$$chr{px1},$xpos,$ypos); }
+    if ( $$chr{px2} ) { draw_regs($opts,$chr_name,$$chr{px2},$xpos+$dimD+$dimE,$ypos); }
+}
+
+sub parse_hex_color
+{
+    my ($color) = @_;
+    if ( !($color=~/^#/) ) { error("Could not parse: $color"); }
+    $color =~ s/^#//;
+    my @vals = split(//, $color);
+    my ($r,$g,$b);
+    if ( @vals==6 )
+    {
+        $r = hex($vals[0].$vals[1]);
+        $g = hex($vals[2].$vals[3]);
+        $b = hex($vals[4].$vals[5]);
+    }
+    elsif ( @vals==3 )
+    {
+        $r = hex($vals[0].$vals[0]);
+        $g = hex($vals[1].$vals[1]);
+        $b = hex($vals[2].$vals[2]);
+    }
+    else { error("Could not parse: $color\n"); }
+    return ($r,$g,$b);
+}
+
+sub scale_color
+{
+    my ($color,$scale) = @_;
+    my ($r1,$g1,$b1) = parse_hex_color($color);
+    my ($r0,$g0,$b0) = parse_hex_color('#aaa');
+    my $r = $scale*($r1-$r0) + $r0;
+    my $g = $scale*($g1-$g0) + $g0;
+    my $b = $scale*($b1-$b0) + $b0;
+    return sprintf("#%0.2x%0.2x%0.2x",$r,$g,$b);
+}
+
+sub draw_regs
+{
+    my ($opts,$chr_name,$regs,$xpos,$ypos) = @_;
+
+    my $svg = $$opts{svg};
+    my $chr = $$opts{chrs}{$chr_name};
+    my $dimL  = $$opts{dimL};
+    my $dimC  = $dimL*($$chr{acen}[2]-$$chr{acen}[0])/$$opts{max_chr_len};
+    my $dimL1 = $dimL*$$chr{acen}[0]/$$opts{max_chr_len};
+    my $dimL2 = $$opts{dimL} - $dimL*$$chr{acen}[2]/$$opts{max_chr_len};
+    my $dimD  = $$opts{dimD};   # arm width
+    my $dimB  = $$opts{dimB};
+    my $dimE  = $$opts{dimE};
+    my $dimE05 = $dimE*0.5;
+    my $dimD05 = $dimD*0.5;
+    my $dimB05 = $dimB*0.5;
+    my $dimC05 = 0.5*$dimC;
+
+    for my $reg (@$regs)
+    {
+        my $sum = 0;
+        my $cmax = undef;
+        for my $c (keys %{$$reg[2]})
+        {
+            $sum += $$reg[2]{$c};
+            if ( !defined $cmax or $$reg[2]{$cmax} < $$reg[2]{$c} ) { $cmax = $c; }
+        }
+        my $color = scale_color($cmax,$$reg[2]{$cmax}/$sum);
+        my $y  = $ypos + $$reg[0];
+        my $dy = $$reg[1] - $$reg[0] + 1;
+        push @$svg, qq[
+            <path d="M$xpos $y
+                     l0 $dy
+                     l$dimD 0
+                     l0 -$dy
+                     l-$dimD 0
+                    "
+                  style="stroke:$color;fill:$color;stroke-width:0;"/> ];
+    }
+
+}
+
+sub hap2color
+{
+    my ($opts,$chr,$hap) = @_;
+    if ( exists($$opts{hap_cols}{$chr}{$hap}) )
+    {
+        if ( !exists($$opts{hap_cols}{'*'}{$hap}) ) 
+        {
+            $$opts{hap_cols}{'*'}{$hap} = $$opts{hap_cols}{$chr}{$hap};
+        }
+        return $$opts{hap_cols}{$chr}{$hap};
+    }
+    elsif ( exists($$opts{hap_cols}{'*'}{$hap}) )
+    {
+        return $$opts{hap_cols}{'*'}{$hap};
+    }
+    if ( !exists($$opts{haps}) ) { $$opts{haps} = {}; }
+    if ( !exists($$opts{haps}{$hap}) )
+    {
+        my $nhaps = scalar keys %{$$opts{haps}};
+        my $color = $$opts{colors}[$nhaps];
+        $$opts{haps}{$hap} = $color;
+    }
+    return $$opts{haps}{$hap};
+}
+
+sub read_dat
+{
+    my ($opts,$file) = @_;
+    open(my $fh,'<',$file) or error("$file: $!");
+    while (my $line=<$fh>)
+    {
+        if ( !($line=~/^SG/) ) { next; }
+        my @items = split(/\s+/,$line);
+        my $chr   = $items[1];
+        my $start = $items[2];
+        my $end   = $items[3];
+        my $hap1  = $items[4];
+        my $hap2  = $items[5];
+        my $col1  = hap2color($opts,$chr,$hap1); 
+        my $col2  = hap2color($opts,$chr,$hap2); 
+        push @{$$opts{chrs}{$chr}{regs1}},[$start,$end,$col1];
+        push @{$$opts{chrs}{$chr}{regs2}},[$start,$end,$col2];
+        my ($smpl,$hap);
+        ($smpl,$hap) = split(/:/,$hap1); $$opts{samples}{$smpl}{$hap} = $col1;
+        ($smpl,$hap) = split(/:/,$hap2); $$opts{samples}{$smpl}{$hap} = $col2;
+    }
+    close($fh);
+}
+
+sub merge_regs
+{
+    my ($opts) = @_;
+    for my $chr (keys %{$$opts{chrs}})
+    {
+        my $dat = $$opts{chrs}{$chr};
+        if ( exists($$dat{regs1}) ) { $$dat{px1} = merge($opts,$dat,$$dat{regs1}); }
+        if ( exists($$dat{regs2}) ) { $$dat{px2} = merge($opts,$dat,$$dat{regs2}); }
+    }
+}
+
+sub merge
+{
+    my ($opts,$chr_dat,$regs) = @_;
+
+    # merge adjacent regions of the same color
+    for (my $i=1; $i<@$regs; $i++)
+    {
+        if ( $$regs[$i-1][2] eq $$regs[$i][2] ) 
+        { 
+            $$regs[$i-1][1] = $$regs[$i][1];
+            splice(@$regs,$i,1);
+            $i--;
+            next; 
+        }
+    }
+    for (my $i=0; $i<@$regs; $i++)
+    {
+        if ( $$regs[$i][1] < $$chr_dat{acen}[0] ) { next; }
+        if ( $$regs[$i][0] > $$chr_dat{acen}[2] ) { next; }
+        if ( $$regs[$i][0] >= $$chr_dat{acen}[0] && $$regs[$i][1] <= $$chr_dat{acen}[2] )
+        {
+            splice(@$regs,$i,1);
+            $i--;
+            next;
+        }
+        if ( $$regs[$i][1] < $$chr_dat{acen}[2] )
+        {
+            $$regs[$i][1] = $$chr_dat{acen}[0];
+            next;
+        }
+        if ( $$regs[$i][0] > $$chr_dat{acen}[0] )
+        {
+            $$regs[$i][0] = $$chr_dat{acen}[2];
+            next;
+        }
+        my $start = $$chr_dat{acen}[2];
+        my $end   = $$regs[$i][1];
+        my $color = $$regs[$i][2];
+        $$regs[$i][1] = $$chr_dat{acen}[0];
+        splice(@$regs,$i+1,0,[$start,$end,$color]);
+    }
+
+    # pixelize
+    my @px = ([0,0,{}]);  # start,end,hash of contributions from colors
+    my $dy = $$opts{max_chr_len}/$$opts{dimL};  # 1px covers $dy base pairs
+    for my $reg (@$regs)
+    {
+        my $px_start = int($$reg[0] / $dy);
+        my $px_end   = int($$reg[1] / $dy);
+        my $color    = $$reg[2];
+        my $contrib  = ($$reg[1] - $$reg[0])/$dy;
+
+        if ( $px_start==$px_end )
+        {
+            if ( $px_end<=$px[-1][1] ) { $px[-1][2]{$color} += $contrib; }
+            else { push @px, [$px_start,$px_end,{$color=>$contrib}]; }
+            next;
+        }
+
+        my $rem_start = 1 - ($$reg[0]/$dy - $px_start);     # fractional remainders
+        my $rem_end   = $$reg[1]/$dy - $px_end;
+
+        if ( $px_start==$px[-1][1] )
+        {
+            $px[-1][2]{$color} += $rem_start;
+        }
+
+        if ( $px_end==$px[-1][1] )
+        {
+            $px[-1][2]{$color} += $rem_end;
+            if ( $px_start+1<$px_end ) { error("really?!\n"); }
+        }
+        elsif ( $px_end>$px[-1][1] )
+        {
+            if ( $rem_start ) { $px_start++; $contrib -= $rem_start; }
+            push @px, [ $px_start, $px_end, { $color=>$contrib } ];
+        }
+        else { error("really?!\n"); }
+    }
+    return \@px;
+}
+
+sub chr_dims
+{
+    my ($opts) = @_;
+
+    # http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/cytoBand.txt.gz
+    my $ktype = q[
+        chr1	121500000	125000000	p11.1	acen
+        chr1	125000000	128900000	q11	acen
+        chr1	243700000	249250621	q44	gneg
+        chr10	38000000	40200000	p11.1	acen
+        chr10	40200000	42300000	q11.1	acen
+        chr10	130600000	135534747	q26.3	gneg
+        chr11	51600000	53700000	p11.11	acen
+        chr11	53700000	55700000	q11	acen
+        chr11	130800000	135006516	q25	gneg
+        chr12	33300000	35800000	p11.1	acen
+        chr12	35800000	38200000	q11	acen
+        chr12	129300000	133851895	q24.33	gneg
+        chr13	16300000	17900000	p11.1	acen
+        chr13	17900000	19500000	q11	acen
+        chr13	110300000	115169878	q34	gneg
+        chr14	16100000	17600000	p11.1	acen
+        chr14	17600000	19100000	q11.1	acen
+        chr14	104000000	107349540	q32.33	gneg
+        chr15	15800000	19000000	p11.1	acen
+        chr15	19000000	20700000	q11.1	acen
+        chr15	98500000	102531392	q26.3	gneg
+        chr16	34600000	36600000	p11.1	acen
+        chr16	36600000	38600000	q11.1	acen
+        chr16	88700000	90354753	q24.3	gneg
+        chr17	22200000	24000000	p11.1	acen
+        chr17	24000000	25800000	q11.1	acen
+        chr17	75300000	81195210	q25.3	gneg
+        chr18	15400000	17200000	p11.1	acen
+        chr18	17200000	19000000	q11.1	acen
+        chr18	73100000	78077248	q23	gneg
+        chr19	24400000	26500000	p11	acen
+        chr19	26500000	28600000	q11	acen
+        chr19	56300000	59128983	q13.43	gpos25
+        chr2	90500000	93300000	p11.1	acen
+        chr2	93300000	96800000	q11.1	acen
+        chr2	237300000	243199373	q37.3	gneg
+        chr20	25600000	27500000	p11.1	acen
+        chr20	27500000	29400000	q11.1	acen
+        chr20	58400000	63025520	q13.33	gneg
+        chr21	10900000	13200000	p11.1	acen
+        chr21	13200000	14300000	q11.1	acen
+        chr21	42600000	48129895	q22.3	gneg
+        chr22	12200000	14700000	p11.1	acen
+        chr22	14700000	17900000	q11.1	acen
+        chr22	49400000	51304566	q13.33	gneg
+        chr3	87900000	91000000	p11.1	acen
+        chr3	91000000	93900000	q11.1	acen
+        chr3	192300000	198022430	q29	gneg
+        chr4	48200000	50400000	p11	acen
+        chr4	50400000	52700000	q11	acen
+        chr4	187100000	191154276	q35.2	gpos25
+        chr5	46100000	48400000	p11	acen
+        chr5	48400000	50700000	q11.1	acen
+        chr5	176600000	180915260	q35.3	gneg
+        chr6	58700000	61000000	p11.1	acen
+        chr6	61000000	63300000	q11.1	acen
+        chr6	164500000	171115067	q27	gneg
+        chr7	58000000	59900000	p11.1	acen
+        chr7	59900000	61700000	q11.1	acen
+        chr7	155100000	159138663	q36.3	gneg
+        chr8	43100000	45600000	p11.1	acen
+        chr8	45600000	48100000	q11.1	acen
+        chr8	139900000	146364022	q24.3	gneg
+        chr9	47300000	49000000	p11.1	acen
+        chr9	49000000	50700000	q11	acen
+        chr9	137400000	141213431	q34.3	gneg
+        chrX	58100000	60600000	p11.1	acen
+        chrX	60600000	63000000	q11.1	acen
+        chrX	147100000	155270560	q28	gneg
+    ];
+    my @lines = split(/\n/,$ktype);
+    my %chrs  = ();
+    my $max_len = 0;
+    for my $line (@lines)
+    {
+        if ( $line =~ /^\s*$/ ) { next; }
+        $line =~ s/^\s*//;
+        $line =~ s/\s*$//;
+        my @items = split(/\s+/,$line);
+        my $chr   = $items[0];
+        my $start = $items[1];
+        my $end   = $items[2];
+        $chr =~ s/^chr//;
+        if ( $items[-1] eq 'acen' )
+        {
+            push @{$chrs{$chr}{acen}},$start;
+            push @{$chrs{$chr}{acen}},$end;
+        }
+        if ( !defined $chrs{$chr}{len} or $chrs{$chr}{len} < $end )
+        { 
+            $chrs{$chr}{len} = $end; 
+        }
+        if ( $max_len < $end ) { $max_len = $end; }
+    }
+    for my $chr (keys %chrs)
+    {
+        splice(@{$chrs{$chr}{acen}},1,1);
+    }
+    $$opts{chrs} = \%chrs;
+    $$opts{max_chr_len} = $max_len;
+}
+
+
+
+
diff --git a/plugins/dosage.c b/plugins/dosage.c
index bbfe2e5..ddc6297 100644
--- a/plugins/dosage.c
+++ b/plugins/dosage.c
@@ -140,7 +140,7 @@ int calc_dosage_GT(bcf1_t *rec)
         float dsg = 0;
         for (j=0; j<nret; j++)
         {
-            if ( ptr[j]==bcf_int32_missing || ptr[j]==bcf_int32_vector_end || ptr[j]==bcf_gt_missing ) break;
+            if ( ptr[j]==bcf_int32_vector_end || bcf_gt_is_missing(ptr[j]) ) break;
             if ( bcf_gt_allele(ptr[j]) ) dsg += 1;
         }
         printf("\t%.1f", j>0 ? dsg : -1);
diff --git a/plugins/fill-tags.c b/plugins/fill-tags.c
new file mode 100644
index 0000000..96f5e33
--- /dev/null
+++ b/plugins/fill-tags.c
@@ -0,0 +1,262 @@
+/* The MIT License
+
+   Copyright (c) 2015 Genome Research Ltd.
+
+   Author: Petr Danecek <pd3 at sanger.ac.uk>
+   
+   Permission is hereby granted, free of charge, to any person obtaining a copy
+   of this software and associated documentation files (the "Software"), to deal
+   in the Software without restriction, including without limitation the rights
+   to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+   copies of the Software, and to permit persons to whom the Software is
+   furnished to do so, subject to the following conditions:
+   
+   The above copyright notice and this permission notice shall be included in
+   all copies or substantial portions of the Software.
+   
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+   IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+   FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+   AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+   LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+   OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+   THE SOFTWARE.
+
+ */
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <getopt.h>
+#include <math.h>
+#include <htslib/hts.h>
+#include <htslib/vcf.h>
+#include "bcftools.h"
+
+#define SET_AN      (1<<0)
+#define SET_AC      (1<<1)
+#define SET_AC_Hom  (1<<2)
+#define SET_AC_Het  (1<<3)
+#define SET_AC_Hemi (1<<4)
+
+typedef struct
+{
+    int nhom, nhet, nhemi, nac;
+}
+counts_t;
+
+typedef struct
+{
+    bcf_hdr_t *in_hdr, *out_hdr;
+    int tags, marr, mcounts, gt_id;
+    int32_t *arr;
+    counts_t *counts;
+}
+args_t;
+
+static args_t args;
+
+const char *about(void)
+{
+    return "Set INFO tags AN, AC, AC_Hom, AC_Het, AC_Hemi.\n";
+}
+
+const char *usage(void)
+{
+    return 
+        "\n"
+        "About: Set INFO tags AN, AC, AC_Hom, AC_Het, AC_Hemi.\n"
+        "Usage: bcftools +fill-tags [General Options] -- [Plugin Options]\n"
+        "Options:\n"
+        "   run \"bcftools plugin\" for a list of common options\n"
+        "\n"
+        "Plugin options:\n"
+        "   -t, --tags LIST         list of output tags. By default, all tags are filled.\n"
+        "\n"
+        "Example:\n"
+        "   bcftools +fill-tags in.bcf -Ob -o out.bcf -- -t AN,AC\n"
+        "   bcftools +fill-tags in.bcf -Ob -o out.bcf\n"
+        "\n";
+}
+
+int parse_tags(args_t *args, const char *str)
+{
+    int i, flag = 0, n_tags;
+    char **tags = hts_readlist(str, 0, &n_tags);
+    for(i=0; i<n_tags; i++)
+    {
+        if ( !strcasecmp(tags[i],"AN") ) flag |= SET_AN;
+        else if ( !strcasecmp(tags[i],"AC") ) flag |= SET_AC;
+        else if ( !strcasecmp(tags[i],"AC_Hom") ) flag |= SET_AC_Hom;
+        else if ( !strcasecmp(tags[i],"AC_Het") ) flag |= SET_AC_Het;
+        else if ( !strcasecmp(tags[i],"AC_Hemi") ) flag |= SET_AC_Hemi;
+        else
+        {
+            fprintf(stderr,"Error parsing \"--tags %s\": the tag \"%s\" is not supported\n", str,tags[i]);
+            exit(1);
+        }
+        free(tags[i]);
+    }
+    if (n_tags) free(tags);
+    return flag;
+}
+
+
+int init(int argc, char **argv, bcf_hdr_t *in, bcf_hdr_t *out)
+{
+    memset(&args,0,sizeof(args_t));
+    args.in_hdr  = in;
+    args.out_hdr = out;
+
+    static struct option loptions[] =
+    {
+        {"tags",1,0,'t'},
+        {0,0,0,0}
+    };
+    char c;
+    while ((c = getopt_long(argc, argv, "?ht:T:l:cd",loptions,NULL)) >= 0)
+    {
+        switch (c) 
+        {
+            case 't': args.tags |= parse_tags(&args,optarg); break;
+            case 'h':
+            case '?':
+            default: error("%s", usage()); break;
+        }
+    }
+    if ( optind != argc ) error(usage());
+    if ( !args.tags ) args.tags |= SET_AN|SET_AC|SET_AC_Hom|SET_AC_Het|SET_AC_Hemi;
+    
+    args.gt_id = bcf_hdr_id2int(args.in_hdr,BCF_DT_ID,"GT");
+    if ( args.gt_id<0 ) error("Error: GT field is not present\n");
+
+    if ( args.tags&SET_AN ) bcf_hdr_append(args.out_hdr, "##INFO=<ID=AN,Number=1,Type=Integer,Description=\"Total number of alleles in called genotypes\">");
+    if ( args.tags&SET_AC ) bcf_hdr_append(args.out_hdr, "##INFO=<ID=AC,Number=A,Type=Integer,Description=\"Allele count in genotypes\">");
+    if ( args.tags&SET_AC_Hom ) bcf_hdr_append(args.out_hdr, "##INFO=<ID=AC_Hom,Number=A,Type=Integer,Description=\"Allele counts in homozygous genotypes\">");
+    if ( args.tags&SET_AC_Het ) bcf_hdr_append(args.out_hdr, "##INFO=<ID=AC_Het,Number=A,Type=Integer,Description=\"Allele counts in heterozygous genotypes\">");
+    if ( args.tags&SET_AC_Hemi ) bcf_hdr_append(args.out_hdr, "##INFO=<ID=AC_Hemi,Number=A,Type=Integer,Description=\"Allele counts in hemizygous genotypes\">");
+
+    return 0;
+}
+
+bcf1_t *process(bcf1_t *rec)
+{
+    int i;
+
+    bcf_unpack(rec, BCF_UN_FMT);
+    bcf_fmt_t *fmt_gt = NULL;
+    for (i=0; i<rec->n_fmt; i++)
+        if ( rec->d.fmt[i].id==args.gt_id ) { fmt_gt = &rec->d.fmt[i]; break; }
+    if ( !fmt_gt ) return rec;    // no GT tag
+
+    hts_expand(int32_t,rec->n_allele,args.marr,args.arr);
+    hts_expand(counts_t,rec->n_allele,args.mcounts,args.counts);
+    memset(args.arr,0,sizeof(*args.arr)*rec->n_allele);
+    memset(args.counts,0,sizeof(*args.counts)*rec->n_allele);
+
+    #define BRANCH_INT(type_t,vector_end) { \
+        for (i=0; i<rec->n_sample; i++) \
+        { \
+            type_t *p = (type_t*) (fmt_gt->p + i*fmt_gt->size); \
+            int ial, als = 0; \
+            for (ial=0; ial<fmt_gt->n; ial++) \
+            { \
+                if ( p[ial]==vector_end ) break; /* smaller ploidy */ \
+                if ( bcf_gt_is_missing(p[ial]) ) break; /* missing allele */ \
+                int idx = bcf_gt_allele(p[ial]); \
+                \
+                if ( idx >= rec->n_allele ) \
+                    error("Incorrect allele (\"%d\") in %s at %s:%d\n",idx,args.in_hdr->samples[i],bcf_seqname(args.in_hdr,rec),rec->pos+1); \
+                als |= (1<<idx);  /* this breaks with too many alleles */ \
+            } \
+            if ( ial==0 ) continue; /* missing alleles */ \
+            int is_hom  = als && !(als & (als-1)); /* only one bit is set */ \
+            int is_hemi = ial==1; \
+            for (ial=0; als; ial++) \
+            { \
+                if ( als&1 ) \
+                { \
+                    if ( !is_hom ) \
+                        args.counts[ial].nhet++; \
+                    else if ( !is_hemi ) \
+                        args.counts[ial].nhom += 2; \
+                    else \
+                        args.counts[ial].nhemi++; \
+                } \
+                als >>= 1; \
+            } \
+        } \
+    }
+    switch (fmt_gt->type) {
+        case BCF_BT_INT8:  BRANCH_INT(int8_t,  bcf_int8_vector_end); break;
+        case BCF_BT_INT16: BRANCH_INT(int16_t, bcf_int16_vector_end); break;
+        case BCF_BT_INT32: BRANCH_INT(int32_t, bcf_int32_vector_end); break;
+        default: error("The GT type is not recognised: %d at %s:%d\n",fmt_gt->type, bcf_seqname(args.in_hdr,rec),rec->pos+1); break;
+    }
+    #undef BRANCH_INT
+    if ( args.tags&SET_AN )
+    {
+        args.arr[0] = 0;
+        for (i=0; i<rec->n_allele; i++)
+            args.arr[0] += args.counts[i].nhet + args.counts[i].nhom + args.counts[i].nhemi;
+        if ( bcf_update_info_int32(args.out_hdr,rec,"AN",args.arr,1)!=0 )
+            error("Error occurred while updating AN at %s:%d\n", bcf_seqname(args.in_hdr,rec),rec->pos+1);
+    }
+    if ( args.tags&SET_AC )
+    {
+        int n = rec->n_allele-1;
+        if ( n>0 )
+        {
+            memset(args.arr,0,sizeof(*args.arr)*rec->n_allele);
+            for (i=1; i<rec->n_allele; i++)
+                args.arr[i] += args.counts[i].nhet + args.counts[i].nhom + args.counts[i].nhemi;
+        }
+        if ( bcf_update_info_int32(args.out_hdr,rec,"AC",args.arr+1,n)!=0 )
+            error("Error occurred while updating AC at %s:%d\n", bcf_seqname(args.in_hdr,rec),rec->pos+1);
+    }
+    if ( args.tags&SET_AC_Het )
+    {
+        int n = rec->n_allele-1;
+        if ( n>0 )
+        {
+            memset(args.arr,0,sizeof(*args.arr)*rec->n_allele);
+            for (i=1; i<rec->n_allele; i++)
+                args.arr[i] += args.counts[i].nhet;
+        }
+        if ( bcf_update_info_int32(args.out_hdr,rec,"AC_Het",args.arr+1,n)!=0 )
+            error("Error occurred while updating AC_Het at %s:%d\n", bcf_seqname(args.in_hdr,rec),rec->pos+1);
+    }
+    if ( args.tags&SET_AC_Hom )
+    {
+        int n = rec->n_allele-1;
+        if ( n>0 )
+        {
+            memset(args.arr,0,sizeof(*args.arr)*rec->n_allele);
+            for (i=1; i<rec->n_allele; i++)
+                args.arr[i] += args.counts[i].nhom;
+        }
+        if ( bcf_update_info_int32(args.out_hdr,rec,"AC_Hom",args.arr+1,n)!=0 )
+            error("Error occurred while updating AC_Hom at %s:%d\n", bcf_seqname(args.in_hdr,rec),rec->pos+1);
+    }
+    if ( args.tags&SET_AC_Hemi )
+    {
+        int n = rec->n_allele-1;
+        if ( n>0 )
+        {
+            memset(args.arr,0,sizeof(*args.arr)*rec->n_allele);
+            for (i=1; i<rec->n_allele; i++)
+                args.arr[i] += args.counts[i].nhemi;
+        }
+        if ( bcf_update_info_int32(args.out_hdr,rec,"AC_Hemi",args.arr+1,n)!=0 )
+            error("Error occurred while updating AC_Hemi at %s:%d\n", bcf_seqname(args.in_hdr,rec),rec->pos+1);
+    }
+    return rec;
+}
+
+void destroy(void)
+{
+    free(args.counts);
+    free(args.arr);
+}
+
+
+
diff --git a/plugins/fixploidy.c b/plugins/fixploidy.c
index ab4c8f5..717ffef 100644
--- a/plugins/fixploidy.c
+++ b/plugins/fixploidy.c
@@ -167,12 +167,15 @@ bcf1_t *process(bcf1_t *rec)
 {
     int i,j, max_ploidy;
 
-    ploidy_query(ploidy, (char*)bcf_seqname(in_hdr,rec), rec->pos, sex2ploidy,NULL,&max_ploidy);
-
     int ngts = bcf_get_genotypes(in_hdr, rec, &gt_arr, &ngt_arr);
+    if ( ngts<0 )
+        return rec;     // GT field not present
+
     if ( ngts % n_sample )
         error("Error at %s:%d: wrong number of GT fields\n",bcf_seqname(in_hdr,rec),rec->pos+1);
 
+    ploidy_query(ploidy, (char*)bcf_seqname(in_hdr,rec), rec->pos, sex2ploidy,NULL,&max_ploidy);
+
     ngts /= n_sample;
     if ( ngts < max_ploidy )
     {
diff --git a/plugins/fixploidy.mk b/plugins/fixploidy.mk
index c564409..c476169 100644
--- a/plugins/fixploidy.mk
+++ b/plugins/fixploidy.mk
@@ -1,2 +1,2 @@
-plugins/fixploidy.so: plugins/fixploidy.c version.h version.c ploidy.h ploidy.c $(HTSDIR)/libhts.so
-	$(CC) $(CFLAGS) $(INCLUDES) -fPIC -shared -o $@ ploidy.c version.c $< -L$(HTSDIR) -lhts
+plugins/fixploidy.so: plugins/fixploidy.c version.h version.c ploidy.h ploidy.c
+	$(CC) $(PLUGIN_FLAGS) $(CFLAGS) $(EXTRA_CPPFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $@ ploidy.c version.c $< $(LIBS)
diff --git a/plugins/impute-info.c b/plugins/impute-info.c
new file mode 100644
index 0000000..c3c74ec
--- /dev/null
+++ b/plugins/impute-info.c
@@ -0,0 +1,163 @@
+/*  plugins/impute-info.c -- adds info metrics to a VCF file.
+
+    Copyright (C) 2015 Genome Research Ltd.
+
+    Author: Shane McCarthy <sm15 at sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+
+/*
+
+Marchini & Howie, Nature Genetics, 11 (July 2010)
+
+Let G_ij in {0,1,2} be the genotype of the ith individual at the
+jth SNP in a study cohort of N samples. Let
+
+    p_ijk = P(G_ij = k | H,G)
+
+be the probability that the genotype at the jth SNP of the ith
+individual is k.
+
+Let the expected allele dosage for the genotype at the jth SNP
+of the ith individual be
+    
+    e_ij = p_ij1 + 2 * p_ij2
+
+and define
+
+    f_ij = p_ij1 + 4 * p_ij2
+
+Let theta_j denote the (unknown) population allele frequency of the jth SNP
+with:
+
+    theta_j = SUM[i=1..N] e_ij / 2 * N
+
+The IMPUTE2 information measure is then:
+
+    if theta_j in (0,1):
+        I(theta_j) = 1 - SUM[i=1..N](f_ij - e_ij^2) / 2 * N * theta_j * (1 - theta_j)
+    else:
+        I(theta_j) = 1
+
+*/
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <htslib/vcf.h>
+#include <math.h>
+#include <getopt.h>
+
+const char *about(void)
+{
+    return "Add imputation information metrics to the INFO field based on selected FORMAT tags.\n";
+}
+
+const char *usage(void)
+{
+    return 
+        "\n"
+        "About: Add imputation information metrics to the INFO field based\n"
+        "       on selected FORMAT tags. Only the IMPUTE2 INFO metric from\n"
+        "       FORMAT/GP tags is currently available.\n"
+        "Usage: bcftools +impute-info [General Options] -- [Plugin Options]\n"
+        "Options:\n"
+        "   run \"bcftools plugin\" for a list of common options\n"
+        "\n"
+        // "Plugin options:\n"
+        // "   -i, --info <list>   information metrics to add [INFO]\n" // [BEAGLE_R2,MACH_R2]
+        // "   -t, --tags <tag>    VCF tags to determine the information from [GP]\n"
+        // "\n"
+        "Example:\n"
+        "   bcftools +impute-info in.vcf\n"
+        "\n";
+}
+
+bcf_hdr_t *in_hdr = NULL, *out_hdr = NULL;
+int gp_type = BCF_HT_REAL;
+uint8_t *buf = NULL;
+int nbuf = 0;   // NB: number of elements, not bytes
+int nrec = 0, nskip_gp = 0, nskip_dip = 0;
+
+int init(int argc, char **argv, bcf_hdr_t *in, bcf_hdr_t *out)
+{
+    in_hdr  = in;
+    out_hdr = out;
+    bcf_hdr_append(out_hdr,"##INFO=<ID=INFO,Number=1,Type=Float,Description=\"IMPUTE2 info score\">");
+    return 0;
+}
+
+bcf1_t *process(bcf1_t *rec)
+{
+    int nval = 0, i, j, nret = bcf_get_format_values(in_hdr,rec,"GP",(void**)&buf,&nbuf,gp_type);
+    if ( nret<0 )
+    {
+        if (!nskip_gp) fprintf(stderr, "[impute-info.c] Warning: info tag not added to sites without GP tag\n");
+        nskip_gp++;
+        return rec; // require FORMAT/GP tag, return site unchanged
+    }
+
+    nret /= rec->n_sample;
+    if ( nret != 3 )
+    {
+        if (!nskip_dip) fprintf(stderr, "[impute-info.c] Warning: info tag not added to sites that are not biallelic diploid\n");
+        nskip_dip++;
+        return rec; // require biallelic diploid, return site unchanged
+    }
+
+    float esum = 0, e2sum = 0, fsum = 0;
+    #define BRANCH(type_t,is_missing,is_vector_end) \
+    { \
+        type_t *ptr = (type_t*) buf; \
+        for (i=0; i<rec->n_sample; i++) \
+        { \
+            float vals[3] = {0,0,0}; \
+            for (j=0; j<nret; j++) \
+            { \
+                if ( is_missing || is_vector_end ) break; \
+                vals[j] = ptr[j]; \
+            } \
+            esum  += vals[1] + 2*vals[2]; \
+            e2sum += (vals[1] + 2*vals[2]) * (vals[1] + 2*vals[2]); \
+            fsum  += vals[1] + 4*vals[2]; \
+            ptr   += nret; \
+            nval++; \
+        } \
+    }
+    switch (gp_type)
+    {
+        case BCF_HT_INT:  BRANCH(int32_t,ptr[j]==bcf_int32_missing,ptr[j]==bcf_int32_vector_end); break;
+        case BCF_HT_REAL: BRANCH(float,bcf_float_is_missing(ptr[j]),bcf_float_is_vector_end(ptr[j])); break;
+    }
+    #undef BRANCH
+
+    float theta = esum / (2 * (float)nval);
+    float info  = (theta>0 && theta<1) ? 1 - (fsum - e2sum) / (2 * (float)nval * theta * (1.0 - theta)) : 1;
+
+    bcf_update_info_float(out_hdr, rec, "INFO", &info, 1);
+    nrec++;
+    return rec;
+}
+
+
+void destroy(void)
+{
+    fprintf(stderr,"Lines total/info-added/unchanged-no-tag/unchanged-not-biallelic-diploid:\t%d/%d/%d/%d\n", nrec+nskip_gp+nskip_dip, nrec, nskip_gp, nskip_dip);
+    free(buf);
+}
diff --git a/plugins/mendelian.c b/plugins/mendelian.c
new file mode 100644
index 0000000..186e3e5
--- /dev/null
+++ b/plugins/mendelian.c
@@ -0,0 +1,248 @@
+/* The MIT License
+
+   Copyright (c) 2015 Genome Research Ltd.
+
+   Author: Petr Danecek <pd3 at sanger.ac.uk>
+   
+   Permission is hereby granted, free of charge, to any person obtaining a copy
+   of this software and associated documentation files (the "Software"), to deal
+   in the Software without restriction, including without limitation the rights
+   to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+   copies of the Software, and to permit persons to whom the Software is
+   furnished to do so, subject to the following conditions:
+   
+   The above copyright notice and this permission notice shall be included in
+   all copies or substantial portions of the Software.
+   
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+   IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+   FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+   AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+   LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+   OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+   THE SOFTWARE.
+
+ */
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <getopt.h>
+#include <math.h>
+#include <htslib/hts.h>
+#include <htslib/vcf.h>
+#include <errno.h>
+#include "bcftools.h"
+
+#define MODE_COUNT     1
+#define MODE_LIST_GOOD 2
+#define MODE_LIST_BAD  4
+#define MODE_DELETE    8
+
+typedef struct
+{
+    int nok, nbad;
+    int imother,ifather,ichild;
+}
+trio_t;
+
+typedef struct _args_t
+{
+    bcf_hdr_t *hdr;
+    int32_t *gt_arr;
+    int mode;
+    int ngt_arr, nrec;
+    trio_t *trios;
+    int ntrios;
+}
+args_t;
+
+static args_t args;
+
+const char *about(void)
+{
+    return "Count Mendelian consistent / inconsistent genotypes.\n";
+}
+
+const char *usage(void)
+{
+    return 
+        "\n"
+        "About: Count Mendelian consistent / inconsistent genotypes.\n"
+        "Usage: bcftools +mendelian [General Options] -- [Plugin Options]\n"
+        "Options:\n"
+        "   run \"bcftools plugin\" for a list of common options\n"
+        "\n"
+        "Plugin options:\n"
+        "   -c, --count             count the number of consistent sites\n"
+        "   -d, --delete            delete inconsistent genotypes (set to \"./.\")\n"
+        "   -l, --list [+x]         list consistent (+) or inconsistent (x) sites\n"
+        "   -t, --trio <m,f,c>      names of mother, father and the child\n"
+        "   -T, --trio-file <file>  list of trios, one per line\n"
+        "\n"
+        "Example:\n"
+        "   bcftools +mendelian in.vcf -- -t Mother,Father,Child -c\n"
+        "\n";
+}
+
+int init(int argc, char **argv, bcf_hdr_t *in, bcf_hdr_t *out)
+{
+    char *trio_samples = NULL, *trio_file = NULL;
+    memset(&args,0,sizeof(args_t));
+    args.hdr  = in;
+    args.mode = 0;
+
+    static struct option loptions[] =
+    {
+        {"trio",1,0,'t'},
+        {"trio-file",1,0,'T'},
+        {"delete",0,0,'d'},
+        {"list",1,0,'l'},
+        {"count",0,0,'c'},
+        {0,0,0,0}
+    };
+    char c;
+    while ((c = getopt_long(argc, argv, "?ht:T:l:cd",loptions,NULL)) >= 0)
+    {
+        switch (c) 
+        {
+            case 'd': args.mode |= MODE_DELETE; break;
+            case 'c': args.mode |= MODE_COUNT; break;
+            case 'l': 
+                if ( !strcmp("+",optarg) ) args.mode |= MODE_LIST_GOOD; 
+                else if ( !strcmp("x",optarg) ) args.mode |= MODE_LIST_BAD; 
+                else error("The argument not recognised: --list %s\n", optarg);
+                break;
+            case 't': trio_samples = optarg; break;
+            case 'T': trio_file = optarg; break;
+            case 'h':
+            case '?':
+            default: error("%s", usage()); break;
+        }
+    }
+    if ( optind != argc ) error(usage());
+    if ( !trio_samples && !trio_file ) error("Expected the -t/T option\n");
+    if ( !args.mode ) error("Expected one of the -c, -d or -l options\n");
+    if ( args.mode&MODE_DELETE && !(args.mode&(MODE_LIST_GOOD|MODE_LIST_BAD)) ) args.mode |= MODE_LIST_GOOD|MODE_LIST_BAD;
+
+    int i, n = 0;
+    char **list;
+    if ( trio_samples )
+    {
+        args.ntrios = 1;
+        args.trios = (trio_t*) calloc(1,sizeof(trio_t));
+        list = hts_readlist(trio_samples, 0, &n);
+        if ( n!=3 ) error("Expected three sample names with -t\n");
+        args.trios[0].imother = bcf_hdr_id2int(args.hdr, BCF_DT_SAMPLE, list[0]);
+        args.trios[0].ifather = bcf_hdr_id2int(args.hdr, BCF_DT_SAMPLE, list[1]);
+        args.trios[0].ichild  = bcf_hdr_id2int(args.hdr, BCF_DT_SAMPLE, list[2]);
+        for (i=0; i<n; i++) free(list[i]);
+        free(list);
+    }
+    if ( trio_file )
+    {
+        list = hts_readlist(trio_file, 1, &n);
+        args.ntrios = n;
+        args.trios = (trio_t*) calloc(n,sizeof(trio_t));
+        for (i=0; i<n; i++)
+        {
+            char *ss = list[i], *se = list[i];
+            while ( *se && *se!=',' ) se++; if ( *se!=',' ) error("Could not parse %s: %s\n",trio_file, ss);
+            *se = 0;
+            args.trios[i].imother = bcf_hdr_id2int(args.hdr, BCF_DT_SAMPLE, ss);
+            if ( args.trios[i].imother<0 ) error("No such sample: \"%s\"\n", ss);
+            ss = ++se; 
+            while ( *se && *se!=',' ) se++; if ( *se!=',' ) error("Could not parse %s\n",trio_file);
+            *se = 0;
+            args.trios[i].ifather = bcf_hdr_id2int(args.hdr, BCF_DT_SAMPLE, ss);
+            if ( args.trios[i].ifather<0 ) error("No such sample: \"%s\"\n", ss);
+            ss = ++se; 
+            while ( *se ) se++; if ( ss==se ) error("Could not parse %s\n",trio_file);
+            args.trios[i].ichild = bcf_hdr_id2int(args.hdr, BCF_DT_SAMPLE, ss);
+            if ( args.trios[i].ichild<0 ) error("No such sample: \"%s\"\n", ss);
+            free(list[i]);
+        }
+        free(list);
+    }
+    return args.mode&(MODE_LIST_GOOD|MODE_LIST_BAD) ? 0 : 1;
+}
+
+bcf1_t *process(bcf1_t *rec)
+{
+    bcf1_t *dflt = args.mode&MODE_LIST_GOOD ? rec : NULL;
+    args.nrec++;
+
+    int ngt = bcf_get_genotypes(args.hdr, rec, &args.gt_arr, &args.ngt_arr);
+    if ( ngt<0 ) return dflt;
+    if ( ngt!=2*bcf_hdr_nsamples(args.hdr) ) return dflt;
+
+    int i, has_bad = 0, needs_update = 0;
+    for (i=0; i<args.ntrios; i++)
+    {
+        int mother,father,child;
+        int32_t a,b,c,d,e,f;
+        trio_t *trio = &args.trios[i];
+
+        a = args.gt_arr[2*trio->imother];
+        b = args.gt_arr[2*trio->imother+1];
+        c = args.gt_arr[2*trio->ifather];
+        d = args.gt_arr[2*trio->ifather+1];
+        e = args.gt_arr[2*trio->ichild];
+        f = args.gt_arr[2*trio->ichild+1];
+        if ( bcf_gt_is_missing(a) || bcf_gt_is_missing(b) ) continue; 
+        if ( bcf_gt_is_missing(c) || bcf_gt_is_missing(d) ) continue; 
+        if ( bcf_gt_is_missing(e) || bcf_gt_is_missing(f) ) continue; 
+
+        mother = (1<<bcf_gt_allele(a)) | (1<<bcf_gt_allele(b));
+        father = (1<<bcf_gt_allele(c)) | (1<<bcf_gt_allele(d));
+        child  = (1<<bcf_gt_allele(e)) | (1<<bcf_gt_allele(f));
+
+        if ( (mother&child) && (father&child) ) 
+        {
+            trio->nok++;
+        }
+        else
+        {
+            trio->nbad++;
+            has_bad = 1;
+            if ( args.mode&MODE_DELETE )
+            {
+                args.gt_arr[2*trio->imother]   = bcf_gt_missing;
+                args.gt_arr[2*trio->imother+1] = bcf_gt_missing;
+                args.gt_arr[2*trio->ifather]   = bcf_gt_missing;
+                args.gt_arr[2*trio->ifather+1] = bcf_gt_missing;
+                args.gt_arr[2*trio->ichild]    = bcf_gt_missing;
+                args.gt_arr[2*trio->ichild+1]  = bcf_gt_missing;
+                needs_update = 1;
+            }
+        }
+    }
+
+    if ( needs_update && bcf_update_genotypes(args.hdr,rec,args.gt_arr,ngt) )
+        error("Could not update GT field at %s:%d\n", bcf_seqname(args.hdr,rec),rec->pos+1);
+
+    if ( args.mode&MODE_LIST_GOOD ) return has_bad ? NULL : rec;
+    if ( args.mode&MODE_LIST_BAD ) return has_bad ? rec : NULL;
+
+    return NULL;
+}
+
+void destroy(void)
+{
+    int i;
+    fprintf(stderr,"# [1]nOK\t[2]nBad\t[3]nSkipped\t[4]Trio\n");
+    for (i=0; i<args.ntrios; i++)
+    {
+        trio_t *trio = &args.trios[i];
+        fprintf(stderr,"%d\t%d\t%d\t%s,%s,%s\n", 
+            trio->nok,trio->nbad,args.nrec-(trio->nok+trio->nbad),
+            bcf_hdr_int2id(args.hdr, BCF_DT_SAMPLE, trio->imother),
+            bcf_hdr_int2id(args.hdr, BCF_DT_SAMPLE, trio->ifather),
+            bcf_hdr_int2id(args.hdr, BCF_DT_SAMPLE, trio->ichild)
+            );
+    }
+    free(args.gt_arr);
+    free(args.trios);
+}
+
+
+
diff --git a/plugins/setGT.c b/plugins/setGT.c
new file mode 100644
index 0000000..55e0f27
--- /dev/null
+++ b/plugins/setGT.c
@@ -0,0 +1,223 @@
+/*  plugins/setGT.c -- set gentoypes to given values
+
+    Copyright (C) 2015 Genome Research Ltd.
+
+    Author: Petr Danecek <pd3 at sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <htslib/vcf.h>
+#include <htslib/vcfutils.h>
+#include <inttypes.h>
+#include <getopt.h>
+#include "bcftools.h"
+
+bcf_hdr_t *in_hdr, *out_hdr;
+int32_t *gts = NULL, mgts = 0;
+int *arr = NULL, marr = 0;
+uint64_t nchanged = 0;
+int tgt_mask = 0, new_mask = 0, new_gt = 0;
+
+#define GT_MISSING   1
+#define GT_PARTIAL  (1<<1)
+#define GT_REF      (1<<2)
+#define GT_MAJOR    (1<<3)
+#define GT_PHASED   (1<<4)
+#define GT_UNPHASED (1<<5)
+#define GT_ALL      (1<<6)
+
+const char *about(void)
+{
+    return "Set genotypes: partially missing to missing, missing to ref/major allele, etc.\n";
+}
+
+const char *usage(void)
+{
+    return 
+        "About: Sets genotypes. The target genotypes can be specified as:\n"
+        "           ./.  .. completely missing (\".\" or \"./.\", depending on ploidy)\n"
+        "           ./x  .. partially missing (e.g., \"./0\" or \".|1\" but not \"./.\")\n"
+        "           .    .. partially or completely missing\n"
+        "           a    .. all genotypes\n"
+        "       and the new genotype can be one of:\n"
+        "           .    .. missing (\".\" or \"./.\", keeps ploidy)\n"
+        "           0    .. reference allele\n"
+        "           M    .. major allele\n"
+        "           p    .. phased genotype\n"
+        "           u    .. unphase genotype and sort by allele (1|0 becomes 0/1)\n"
+        "Usage: bcftools +setGT [General Options] -- [Plugin Options]\n"
+        "Options:\n"
+        "   run \"bcftools plugin\" for a list of common options\n"
+        "\n"
+        "Plugin options:\n"
+        "   -n, --new-gt <type>         Genotypes to set, see above\n"
+        "   -t, --target-gt <type>      Genotypes to change, see above\n"
+        "\n"
+        "Example:\n"
+        "   # set missing genotypes (\"./.\") to phased ref genotypes (\"0|0\")\n"
+        "   bcftools +setGT in.vcf -- -t . -n 0p\n"
+        "\n"
+        "   # set partially missing genotypes to completely missing\n"
+        "   bcftools +setGT in.vcf -- -t ./x -n .\n"
+        "\n";
+}
+
+
+int init(int argc, char **argv, bcf_hdr_t *in, bcf_hdr_t *out)
+{
+    int c;
+    static struct option loptions[] =
+    {
+        {"new-gt",1,0,'n'},
+        {"target-gt",0,0,'t'},
+        {0,0,0,0}
+    };
+    while ((c = getopt_long(argc, argv, "?hn:t:",loptions,NULL)) >= 0)
+    {
+        switch (c) 
+        {
+            case 'n': new_mask = bcf_gt_phased(0); 
+                if ( strchr(optarg,'.') ) new_mask |= GT_MISSING;
+                if ( strchr(optarg,'0') ) new_mask |= GT_REF;
+                if ( strchr(optarg,'M') ) new_mask |= GT_MAJOR;
+                if ( strchr(optarg,'p') ) new_mask |= GT_PHASED;
+                if ( strchr(optarg,'u') ) new_mask |= GT_UNPHASED;
+                break;
+            case 't':
+                if ( !strcmp(optarg,".") ) tgt_mask |= GT_MISSING|GT_PARTIAL;
+                if ( !strcmp(optarg,"./x") ) tgt_mask |= GT_PARTIAL;
+                if ( !strcmp(optarg,"./.") ) tgt_mask |= GT_MISSING;
+                if ( !strcmp(optarg,"a") ) tgt_mask |= GT_ALL;
+                break;
+            case 'h':
+            case '?':
+            default: fprintf(stderr,"%s", usage()); exit(1); break;
+        }
+    }
+    in_hdr  = in;
+    out_hdr = out;
+
+    if ( !new_mask ) error("Expected -n option\n");
+    if ( !tgt_mask ) error("Expected -t option\n");
+
+    if ( new_mask & GT_MISSING ) new_gt = bcf_gt_missing;
+    if ( new_mask & GT_REF ) new_gt = new_mask&GT_PHASED ? bcf_gt_phased(0) : bcf_gt_unphased(0);
+
+    return 0;
+}
+
+bcf1_t *process(bcf1_t *rec)
+{
+    if ( !rec->n_sample ) return rec;
+
+    int ngts = bcf_get_genotypes(in_hdr, rec, &gts, &mgts);
+    ngts /= rec->n_sample;
+    int i, j, changed = 0;
+    
+    // Calculating allele frequency for each allele and determining major allele
+    // only do this if use_major is true
+    int an = 0, maxAC = -1, majorAllele = -1;
+    if ( new_mask & GT_MAJOR )
+    {
+        hts_expand(int,rec->n_allele,marr,arr);
+        int ret = bcf_calc_ac(in_hdr,rec,arr,BCF_UN_FMT);
+        if ( ret<= 0 )
+            error("Could not calculate allele count at %s:%d\n", bcf_seqname(in_hdr,rec),rec->pos+1);
+
+        for(i=0; i < rec->n_allele; ++i)
+        {
+            an += arr[i];
+            if (arr[i] > maxAC)
+            {
+                maxAC = arr[i];
+                majorAllele = i;
+            }
+        }
+
+        // replacing new_gt by major allele
+        new_gt = new_mask & GT_PHASED ?  bcf_gt_phased(majorAllele) : bcf_gt_unphased(majorAllele);
+    }
+
+    // replace gts
+    for (i=0; i<rec->n_sample; i++)
+    {
+        int ploidy = 0, nmiss = 0;
+        int32_t *ptr = gts + i*ngts;
+        for (j=0; j<ngts; j++)
+        {
+            if ( ptr[j]==bcf_int32_vector_end ) break;
+            ploidy++;
+            if ( ptr[j]==bcf_gt_missing ) nmiss++;
+        }
+
+        int do_set = 0;
+        if ( tgt_mask&GT_ALL ) do_set = 1;
+        else if ( tgt_mask&GT_PARTIAL && nmiss ) do_set = 1;
+        else if ( tgt_mask&GT_MISSING && ploidy==nmiss ) do_set = 1;
+
+        if ( !do_set ) continue;
+
+        if ( new_mask&GT_UNPHASED )
+        {
+            for (j=0; j<ngts; j++)
+            {
+                if ( ptr[j]==bcf_int32_vector_end ) break;
+                if ( !bcf_gt_is_phased(ptr[j]) ) continue;
+                ptr[j] = bcf_gt_unphased(bcf_gt_allele(ptr[j]));    // remove phasing
+                changed++;
+            }
+
+            // insertion sort
+            int k, l;
+            for (k=1; k<j; k++)
+            {
+                int32_t x = ptr[k];
+                l = k;
+                while ( l>0 && ptr[l-1]>x )
+                {
+                    ptr[l] = ptr[l-1];
+                    l--;
+                }
+                ptr[l] = x;
+            }
+            continue;
+        }
+
+        for (j=0; j<ngts; j++)
+        {
+            if ( ptr[j]==bcf_int32_vector_end ) break;
+            ptr[j] = new_gt;
+            changed++;
+        }
+    }
+    nchanged += changed;
+    if ( changed ) bcf_update_genotypes(out_hdr, rec, gts, ngts*rec->n_sample);
+    return rec;
+}
+
+void destroy(void)
+{
+    free(arr);
+    fprintf(stderr,"Filled %"PRId64" alleles\n", nchanged);
+    free(gts);
+}
+
+
diff --git a/plugins/tag2tag.c b/plugins/tag2tag.c
index 4081bd7..ec89565 100644
--- a/plugins/tag2tag.c
+++ b/plugins/tag2tag.c
@@ -1,4 +1,4 @@
-/*  plugins/fill-AN-AC.c -- fills AN and AC INFO fields.
+/*  plugins/tag2tag.c -- Convert between similar tags, such as GL and GP.
 
     Copyright (C) 2014 Genome Research Ltd.
 
@@ -32,10 +32,12 @@ DEALINGS IN THE SOFTWARE.  */
 
 
 #define GP_TO_GL 1
+#define GL_TO_PL 2
 
 static int mode = 0, drop_source_tag = 0;
 static bcf_hdr_t *in_hdr, *out_hdr;
 static float *farr = NULL;
+static int32_t *iarr = NULL;
 static int mfarr = 0;
 
 const char *about(void)
@@ -55,6 +57,7 @@ const char *usage(void)
         "Plugin options:\n"
 //todo        "       --gl-to-gp    convert FORMAT/GL to FORMAT/GP\n" 
         "       --gp-to-gl    convert FORMAT/GP to FORMAT/GL\n"
+        "       --gl-to-pl    convert FORMAT/GL to FORMAT/PL\n"
         "   -r, --replace     drop the source tag\n"
         "\n"
         "Example:\n"
@@ -77,6 +80,7 @@ int init(int argc, char **argv, bcf_hdr_t *in, bcf_hdr_t *out)
     {
         {"replace",0,0,'r'},
         {"gp-to-gl",0,0,1},
+        {"gl-to-pl",0,0,2},
         {0,0,0,0}
     };
     char c;
@@ -85,6 +89,7 @@ int init(int argc, char **argv, bcf_hdr_t *in, bcf_hdr_t *out)
         switch (c) 
         {
             case  1 : mode = GP_TO_GL; break;
+            case  2 : mode = GL_TO_PL; break;
             case 'r': drop_source_tag = 1; break;
             case 'h':
             case '?':
@@ -98,6 +103,8 @@ int init(int argc, char **argv, bcf_hdr_t *in, bcf_hdr_t *out)
 
     if ( mode==GP_TO_GL )
         init_header(out_hdr,drop_source_tag?"GP":NULL,BCF_HL_FMT,"##FORMAT=<ID=GL,Number=G,Type=Float,Description=\"Genotype Likelihoods\">");
+    else if ( mode==GL_TO_PL )
+        init_header(out_hdr,drop_source_tag?"GL":NULL,BCF_HL_FMT,"##FORMAT=<ID=PL,Number=G,Type=Integer,Description=\"Phred scaled genotype likelihoods\">");
 
     return 0;
 }
@@ -117,12 +124,39 @@ bcf1_t *process(bcf1_t *rec)
         if ( drop_source_tag )
             bcf_update_format_float(out_hdr,rec,"GP",NULL,0);
     }
+    else if ( mode==GL_TO_PL )
+    {
+        n = bcf_get_format_float(in_hdr,rec,"GL",&farr,&mfarr);
+        if(n < 0){
+            fprintf(stderr, "Could not read tag: GL\n");
+            exit(1);
+        }
+            
+        
+        // create extra space to store converted data
+        iarr = (int32_t*) malloc(n * sizeof(int32_t));
+        if(!iarr) n = -4;
+
+        for (i=0; i<n; i++)
+        {
+            if ( bcf_float_is_missing(farr[i]) )
+                iarr[i] = bcf_int32_missing;
+            else if ( bcf_float_is_vector_end(farr[i]) )
+                iarr[i] = bcf_int32_vector_end;
+            else
+                iarr[i] = lroundf(-10 * farr[i]);
+        }
+        bcf_update_format_int32(out_hdr,rec,"PL",iarr,n);
+        if ( drop_source_tag )
+            bcf_update_format_float(out_hdr,rec,"GL",NULL,0);
+    }
     return rec;
 }
 
 void destroy(void)
 {
     free(farr);
+    free(iarr);
 }
 
 
diff --git a/plugins/vcf2sex.c b/plugins/vcf2sex.c
index bad4c3d..b9ce69d 100644
--- a/plugins/vcf2sex.c
+++ b/plugins/vcf2sex.c
@@ -31,18 +31,42 @@
 #include <htslib/regidx.h>
 #include <htslib/synced_bcf_reader.h>
 #include <htslib/vcfutils.h>
+#include <inttypes.h>
 #include "bcftools.h"
 #include "ploidy.h"
 
+#define GUESS_GT 1
+#define GUESS_PL 2
+#define GUESS_GL 3
+
+typedef struct
+{
+    uint64_t nhet, nhom, nmiss;
+}
+count_t;
+
+typedef struct
+{
+    char *chr;
+    uint32_t start, end;
+    int *sex2ploidy;    // sex ploidies
+    count_t *counts;    // per-sample counts: counts[isample]
+}
+reg_stats_t;
+
 typedef struct
 {
     int nsites, nsex, *sex2ploidy, dflt_ploidy, max_ploidy, guess;
-    int ncounts, *counts, nsample, verbose;
+    count_t *bg_counts;         // background het/hom counts for regions with the same ploidy in all sexes
+    reg_stats_t *reg_stats;     // counts for all regions, used with -g
+    int nreg_stats, nsample, verbose;
+    int *counts, ncounts;       // number of observed GTs with given ploidy, used when -g is not given
     float *sex2prob, min_hets;
-    int32_t *gts, ngts;
+    int32_t *gts, ngts, *pls, npls;
     bcf_srs_t *sr;
     bcf_hdr_t *hdr;
     ploidy_t *ploidy;
+    char *background;
 }
 args_t;
 
@@ -55,15 +79,23 @@ const char *usage(void)
 {
     return 
         "\n"
-        "About: Determine sample sex by either checking the presence of haploid/diploid\n"
-        "       genotypes (requires correct ploidy in the VCF) or by counting homs/hets\n"
-        "       in haploid regions.\n"
+        "About: Determine sample sex by checking the presence of haploid/diploid genotypes\n"
+        "       (requires correct ploidy in the VCF). Alternatively, determine the sex by\n"
+        "       counting homs/hets (-g GT) or most likely hom/het genotypes (-g PL) in haploid\n"
+        "       regions. With -g, a region is deemed haploid when the fraction of hets in the\n"
+        "       region is significantly smaller than in the background region. For example,\n"
+        "       the default \"-m 0.3\" requires the het rate to be at least 30% of the background\n"
+        "       rate. If the background region is disabled (\"-b -\"), the threshold -m is interpreted\n"
+        "       directly as the minimum fraction of hets in the region.\n"
+        "\n"
         "Usage: bcftools +vcf2sex <file.vcf.gz> -- [Plugin Options]\n"
         "Plugin options:\n"
-        "   -g, --guess             do not trust genotypes ploidy, count hom/hets\n"
-        "   -m, --min-hets <float>  minimum fraction of hets in diploid regions [0.05]\n"
-        "   -n, --nsites <int>      number of sites to check per region (ignored with -g) [10]\n"
-        "   -p, --ploidy <file>     space/tab-delimited list of CHROM,FROM,TO,SEX,PLOIDY\n"
+        "   -b, --background <region>   diploid region to determine normal hom/hets counts [X:60001-2699520]\n"
+        "   -g, --guess <tag>           determine ploidy by counting hom/hets (GT) or most likely genotypes (PL or GL)\n"
+        "   -m, --min-hets <float>      minimum fraction of hets in diploid regions [0.3]\n"
+        "   -n, --nsites <int>          number of sites to check per region (ignored with -g) [10]\n"
+        "   -p, --ploidy <file>         space/tab-delimited list of CHROM,FROM,TO,SEX,PLOIDY\n"
+        "   -v, --verbose               print debugging information\n"
         "\n"
         "Example:\n"
         "   # Default ploidy, if -p not given. Unlisted regions have ploidy 2\n"
@@ -74,9 +106,36 @@ const char *usage(void)
         "   \n"
         "   bcftools +vcf2sex in.vcf.gz\n"
         "   bcftools +vcf2sex in.vcf.gz -- -n 10\n"
+        "   bcftools +vcf2sex in.vcf.gz -- -g GT\n"
         "\n";
 }
 
+reg_stats_t *expand_regs(args_t *args, char *seq, uint32_t start, uint32_t end)
+{
+    args->nreg_stats++;
+    args->reg_stats = (reg_stats_t*) realloc(args->reg_stats,sizeof(reg_stats_t)*args->nreg_stats);
+    reg_stats_t *stats = args->reg_stats + args->nreg_stats-1;
+    stats->chr = strdup(seq);
+    stats->start = start;
+    stats->end = end;
+    stats->sex2ploidy = (int*) malloc(sizeof(int)*args->nsex);
+    memcpy(stats->sex2ploidy,args->sex2ploidy,sizeof(int)*args->nsex);
+    stats->counts = (count_t*) calloc(args->nsample,sizeof(count_t));
+    return stats;
+}
+void destroy_regs(args_t *args)
+{   
+    int i;
+    for (i=0; i<args->nreg_stats; i++)
+    {
+        free(args->reg_stats[i].chr);
+        free(args->reg_stats[i].counts);
+        free(args->reg_stats[i].sex2ploidy);
+    }
+    free(args->reg_stats);
+    args->nreg_stats = 0;
+}
+
 int process_region_precise(args_t *args, char *seq, regitr_t *itr)
 {
     int k = 1;
@@ -111,8 +170,10 @@ int process_region_precise(args_t *args, char *seq, regitr_t *itr)
             int32_t *gts = args->gts + ngts*ismpl;
             int igt, ploidy = 0;
             for (igt=0; igt<ngts; igt++)
-                if ( gts[igt]==bcf_gt_missing || gts[igt]==bcf_int32_missing || gts[igt]==bcf_int32_vector_end ) break;
+            {
+                if ( gts[igt]==bcf_int32_vector_end || bcf_gt_is_missing(gts[igt]) ) break;
                 else ploidy++;
+            }
             args->counts[ismpl*(args->max_ploidy+1) + ploidy]++;
             if ( args->verbose )
                 fprintf(stderr,"%s:%d\t%s\tploidy=%d\n", seq,rec->pos+1,args->hdr->samples[ismpl],ploidy);
@@ -137,85 +198,212 @@ int process_region_precise(args_t *args, char *seq, regitr_t *itr)
 
 int process_region_guess(args_t *args, char *seq, regitr_t *itr)
 {
-    int ismpl, k = 1;
-    uint32_t start = itr->reg[itr->i].start, end = itr->reg[itr->i].end;
-    while ( itr->i+k<itr->n && start==itr->reg[itr->i+k].start && end==itr->reg[itr->i+k].end ) k++;
-    
-    int ret = ploidy_query(args->ploidy, seq, start, args->sex2ploidy, NULL, NULL);
-    assert(ret);
+    int kitr = 1;
+    uint32_t start = 0, end = INT_MAX;
+    reg_stats_t *stats = NULL;
 
-    memset(args->counts,0,args->ncounts*sizeof(int));
+    // set the start and the end position
+    if ( itr )
+    {
+        start = itr->reg[itr->i].start;
+        end   = itr->reg[itr->i].end;
+
+        // flush all records with the same coordinates
+        while ( itr->i+kitr<itr->n && start==itr->reg[itr->i+kitr].start && end==itr->reg[itr->i+kitr].end ) kitr++;
+
+        int min,max,ret = ploidy_query(args->ploidy, seq, start, args->sex2ploidy, &min, &max);
+        assert(ret);
+        stats = expand_regs(args, seq,start,end);
+    }
+    else
+    {
+        // background region
+        int spos, epos;
+        const char *ptr = hts_parse_reg(args->background, &spos, &epos);
+        if ( !ptr )
+            error("Could not parse the region: %s\n", args->background);
+        seq = (char*) malloc(ptr - args->background + 1);
+        memcpy(seq,args->background,ptr-args->background);
+        seq[ptr-args->background] = 0;
+        start = spos;
+        end   = epos;
+    }
+
+    if ( bcf_sr_seek(args->sr,seq,start)!=0 ) 
+    {
+        // sequence not present
+        if ( !itr ) free(seq);
+        return kitr;
+    }
+
+    int ismpl, rid = bcf_hdr_name2id(args->hdr,seq);
+    if ( !itr ) free(seq);
 
-    if ( bcf_sr_seek(args->sr,seq,start)!=0 ) return k;   // sequence not present
-    int rid = bcf_hdr_name2id(args->hdr,seq);
     while ( bcf_sr_next_line(args->sr) )
     {
         bcf1_t *rec = bcf_sr_get_line(args->sr,0);
         if ( rec->rid!=rid || rec->pos > end ) break;
 
-        bcf_fmt_t *fmt = bcf_get_fmt(args->hdr, rec, "GT");
+        if ( args->guess & GUESS_GT )   // use GTs to guess the ploidy
+        {
+            bcf_fmt_t *fmt = bcf_get_fmt(args->hdr, rec, "GT");
+            if ( !fmt ) continue;
+            for (ismpl=0; ismpl<args->nsample; ismpl++)
+            {
+                count_t *counts = stats ? &stats->counts[ismpl] : &args->bg_counts[ismpl];
+                int gt = bcf_gt_type(fmt, ismpl, NULL,NULL);
+                if ( gt==GT_UNKN ) counts->nmiss++;
+                else if ( gt==GT_HET_RA || gt==GT_HET_AA ) counts->nhet++;
+                else counts->nhom++;
+            }
+        }
+        else    // use PLs to guess the ploidy
+        {
+            int gl2pl = args->guess & GUESS_PL ? 1 : -1;
+            int npl = bcf_get_format_int32(args->hdr,rec,args->guess&GUESS_PL?"PL":"GL",&args->pls,&args->npls);
+            if ( npl<=0 ) continue;
+            npl /= args->nsample;
+            for (ismpl=0; ismpl<args->nsample; ismpl++)
+            {
+                int32_t *ptr = args->pls + ismpl*npl;
+                int phom = INT_MAX, phet = INT_MAX, ial, jal, k = 0;
+                for (ial=0; ial<rec->n_allele; ial++)
+                {
+                    for (jal=0; jal<ial; jal++)
+                    {
+                        if ( ptr[k] == bcf_int32_missing || ptr[k] == bcf_int32_vector_end )  break;
+                        ptr[k] *= gl2pl;
+                        if ( phet > ptr[k] ) phet = ptr[k];
+                        k++;
+                    }
+                    if ( ptr[k] == bcf_int32_missing || ptr[k] == bcf_int32_vector_end )  break;
+                    ptr[k] *= gl2pl;
+                    if ( phom > ptr[k] ) phom = ptr[k];
+                    k++;
+                }
+                count_t *counts = stats ? &stats->counts[ismpl] : &args->bg_counts[ismpl];
+                if ( k == rec->n_allele ) counts->nhom++;   // haploid
+                else if ( phet == phom || k != rec->n_allele*(rec->n_allele+1)/2 ) counts->nmiss++;
+                else if ( phet < phom ) counts->nhet++;
+                else counts->nhom++;
+            }
+        }
+    }
+    return kitr;
+}
+
+void sex2prob_guess(args_t *args)
+{
+    int ismpl, ireg; 
+
+    // get numbers from the background region
+    if ( args->background )
+    {
+        process_region_guess(args, NULL, NULL);
+
+        if ( args->verbose )
+            printf("# [1]BGR\t[2]Region\t[3]Sample\t[4]Het fraction\t[5]nHet\t[6]nHom\t[7]nMissing\n");
+
         for (ismpl=0; ismpl<args->nsample; ismpl++)
         {
-            int gt = bcf_gt_type(fmt, ismpl, NULL,NULL);
-            if ( gt==GT_UNKN ) args->counts[ismpl*3+0]++;       // missing
-            else if ( gt==GT_HET_RA || gt==GT_HET_AA ) args->counts[ismpl*3+1]++;   // het
-            else args->counts[ismpl*3+2]++; // hom
+            uint64_t nhom  = args->bg_counts[ismpl].nhom;
+            uint64_t nhet  = args->bg_counts[ismpl].nhet;
+            uint64_t nmiss = args->bg_counts[ismpl].nmiss;
+            if ( nhom+nhet==0 )
+                fprintf(stderr,"Warning: The sample %s has no variants in the background region %s\n", args->hdr->samples[ismpl],args->background);
+
+            float bg_het = (float)nhet/(nhom+nhet);
+            if ( args->verbose )
+                printf("BGR\t%s\t%s\t%f\t%"PRId64"\t%"PRId64"\t%"PRId64"\n", args->background,args->hdr->samples[ismpl],bg_het,nhet,nhom,nmiss);
         }
     }
 
-    for (ismpl=0; ismpl<args->nsample; ismpl++)
+    // a very simple heuristics to determine sex by counting hets/homs/missing sites
+    for (ireg=0; ireg<args->nreg_stats; ireg++)
     {
-        float sum = 0, *probs = args->sex2prob + ismpl*args->nsex;
-        int i, *counts = args->counts + ismpl*(args->max_ploidy+1);
-        float fhet = (counts[1]+counts[2]) ? (float)counts[1]/(counts[1]+counts[2]) : 0;
-        for (i=0; i<args->max_ploidy+1; i++) sum += counts[i];
-        for (i=0; i<args->nsex; i++)
+        reg_stats_t *stats = &args->reg_stats[ireg];
+        for (ismpl=0; ismpl<args->nsample; ismpl++)
         {
-            // a very simple heuristics to determine sex by counting hets/homs/missing sites,
-            // in human nhet/nhom ~ 0.2
-            int ploidy = args->sex2ploidy[i];
-            float prob = 1;
-            if ( ploidy==0 )
-                prob = sum ? counts[0] / sum : 1;   // fraction of missing sites
-            else if ( ploidy==1 )
+            uint64_t nhom  = stats->counts[ismpl].nhom;
+            uint64_t nhet  = stats->counts[ismpl].nhet;
+            uint64_t nmiss = stats->counts[ismpl].nmiss;
+            float fhet   = nhom+nhet ? (float)nhet/(nhom+nhet) : 0;
+
+            float bg_fhet = -1;
+            if ( args->background )
             {
-                if ( counts[1]+counts[2] ) prob = fhet > args->min_hets ? 0.1 : 0.9;
-                prob *= sum ? 1 - counts[0] / sum : 1./args->nsex;
+                uint64_t bg_nhom  = args->bg_counts[ismpl].nhom;
+                uint64_t bg_nhet  = args->bg_counts[ismpl].nhet;
+                bg_fhet = bg_nhom+bg_nhet ? (float)bg_nhet/(bg_nhom+bg_nhet) : 0;
             }
-            else 
+
+            if ( args->verbose )
+                printf("REG\t%s:%d-%d\t%s\t%f\t%"PRId64"\t%"PRId64"\t%"PRId64"\n", stats->chr,stats->start+1,stats->end+1,args->hdr->samples[ismpl],fhet,nhet,nhom,nmiss);
+
+            int i, ntot = nhom + nhet + nmiss;
+            if ( !ntot ) continue;
+
+            float *probs = args->sex2prob + ismpl*args->nsex;
+            for (i=0; i<args->nsex; i++)
             {
-                if ( counts[1]+counts[2] ) prob = fhet > args->min_hets ? 0.9 : 0.1;
-                prob *= sum ? 1 - counts[0] / sum : 1./args->nsex;
+                int ploidy = stats->sex2ploidy[i];
+                float prob;
+                if ( ploidy==0 )
+                    prob = (float) nmiss / ntot;   // fraction of missing sites
+                else if ( ploidy==1 )
+                {
+                    // NB: these numbers (0.1,0.9) are made up, to be improved
+                    if ( bg_fhet<0 )
+                        prob = fhet > args->min_hets ? 0.1 : 0.9;
+                    else
+                        prob = fhet > args->min_hets*bg_fhet ? 0.1 : 0.9;
+                    prob *= 1 - (float)nmiss / ntot;
+                }
+                else 
+                {
+                    if ( bg_fhet<0 )
+                        prob = fhet > args->min_hets ? 0.9 : 0.1;
+                    else
+                        prob = fhet > args->min_hets*bg_fhet ? 0.9 : 0.1;
+                    prob *= 1 - (float)nmiss / ntot;
+                }
+                probs[i] *= prob;
             }
-            probs[i] *= prob;
         }
-        if ( args->verbose )
-            printf("DBG\t%s:%d-%d\t%s\t%f\t%d\t%d\t%d\n", seq,start+1,end+1,args->hdr->samples[ismpl], fhet,counts[0],counts[1],counts[2]);
     }
-
-    return k;
 }
 
 int run(int argc, char **argv)
 {
     args_t *args  = (args_t*) calloc(1,sizeof(args_t));
     args->nsites = 10;
-    args->min_hets = 0.05;
+    args->min_hets = 0.3;
+    args->background = "X:60001-2699520";
     static struct option loptions[] =
     {
         {"verbose",1,0,'v'},
         {"ploidy",1,0,'p'},
         {"nsites",1,0,'n'},
-        {"guess",0,0,'g'},
+        {"guess",1,0,'g'},
         {"min-hets",1,0,'m'},
+        {"background",1,0,'b'},
         {0,0,0,0}
     };
     char c, *tmp, *ploidy_fname = NULL;
-    while ((c = getopt_long(argc, argv, "p:n:gm:v",loptions,NULL)) >= 0)
+    while ((c = getopt_long(argc, argv, "p:n:g:m:vb:",loptions,NULL)) >= 0)
     {
         switch (c) {
+            case 'b': 
+                if ( !strcmp("-",optarg) ) args->background = NULL;
+                else args->background = optarg; 
+                break; 
             case 'v': args->verbose = 1; break; 
-            case 'g': args->guess = 1; break;
+            case 'g':
+                if ( !strcasecmp(optarg,"GT") ) args->guess = GUESS_GT;
+                else if ( !strcasecmp(optarg,"PL") ) args->guess = GUESS_PL;
+                else if ( !strcasecmp(optarg,"GL") ) args->guess = GUESS_GL;
+                else error("The argument not recognised, expected --guess GT, --guess PL or --guess GL: %s\n", optarg);
+                break;
             case 'm': 
                 args->min_hets = strtod(optarg,&tmp); 
                 if ( *tmp ) error("Unexpected argument to --min-hets: %s\n", optarg);
@@ -232,7 +420,8 @@ int run(int argc, char **argv)
 
     args->sr = bcf_sr_init();
     args->sr->require_index = 1;
-    if ( !argv[0] || !bcf_sr_add_reader(args->sr,argv[0]) ) error("%s", usage());
+    if ( !argv[0] ) error("%s", usage());
+    if ( !bcf_sr_add_reader(args->sr,argv[0]) ) error("Error: %s\n", bcf_sr_strerror(args->sr->errnum));
     args->hdr = args->sr->readers[0].header;
     args->nsample = bcf_hdr_nsamples(args->hdr);
  
@@ -256,14 +445,16 @@ int run(int argc, char **argv)
     if ( args->guess && args->max_ploidy > 2 ) error("Sorry, ploidy %d not supported with -g\n", args->max_ploidy);
     args->ncounts = args->nsample * ((args->max_ploidy>2 ? args->max_ploidy : 2)+1);
     args->counts = (int*) malloc(sizeof(int)*args->ncounts);
+    args->bg_counts = (count_t*) calloc(args->nsample,sizeof(count_t));
     args->sex2prob = (float*) calloc(args->nsample*args->nsex,sizeof(float));
 
     int i, nseq;
     for (i=0; i<args->nsample*args->nsex; i++) args->sex2prob[i] = 1;
 
     if ( args->verbose && args->guess )
-        printf("# [1]DBG\t[2]Region\t[3]Sample\t[4]HET fraction\t[5]nHet\t[6]nHom\t[7]nMissing\n");
+        printf("# [1]REG\t[2]Region\t[3]Sample\t[4]Het fraction\t[5]nHet\t[6]nHom\t[7]nMissing\n");
 
+    // First get the counts from expected haploid regions
     regidx_t *idx = ploidy_regions(args->ploidy);
     char **seqs = regidx_seq_names(idx, &nseq);
     for (i=0; i<nseq; i++)
@@ -271,11 +462,16 @@ int run(int argc, char **argv)
         regitr_t itr;
         regidx_overlap(idx, seqs[i], 0, UINT32_MAX, &itr);
         while ( itr.i < itr.n )
+        {
             if ( args->guess )
                 itr.i += process_region_guess(args, seqs[i], &itr);
             else
                 itr.i += process_region_precise(args, seqs[i], &itr);
+        }
     }
+    // Get the counts from a PAR (the background diploid region) and see if the fraction
+    // of hets is different
+    if ( args->guess ) sex2prob_guess(args);
 
     for (i=0; i<args->nsample; i++)
     {
@@ -298,9 +494,12 @@ int run(int argc, char **argv)
    
     bcf_sr_destroy(args->sr);
     ploidy_destroy(args->ploidy);
+    destroy_regs(args);
     free(args->sex2ploidy);
     free(args->counts);
+    free(args->bg_counts);
     free(args->gts);
+    free(args->pls);
     free(args->sex2prob);
     free(args);
     return 0;
diff --git a/plugins/vcf2sex.mk b/plugins/vcf2sex.mk
index a3720aa..fa3d999 100644
--- a/plugins/vcf2sex.mk
+++ b/plugins/vcf2sex.mk
@@ -1,2 +1,2 @@
-plugins/vcf2sex.so: plugins/vcf2sex.c version.h version.c ploidy.h ploidy.c $(HTSDIR)/libhts.so
-	$(CC) $(CFLAGS) $(INCLUDES) -fPIC -shared -o $@ ploidy.c version.c $< -L$(HTSDIR) -lhts
+plugins/vcf2sex.so: plugins/vcf2sex.c version.h version.c ploidy.h ploidy.c
+	$(CC) $(PLUGIN_FLAGS) $(CFLAGS) $(EXTRA_CPPFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $@ ploidy.c version.c $< $(LIBS)
diff --git a/polysomy.c b/polysomy.c
index e5a94dc..c5a5394 100644
--- a/polysomy.c
+++ b/polysomy.c
@@ -1,19 +1,19 @@
 /* The MIT License
 
-   Copyright (c) 2013-2014 Genome Research Ltd.
+   Copyright (c) 2013-2015 Genome Research Ltd.
 
    Author: Petr Danecek <pd3 at sanger.ac.uk>
-   
+
    Permission is hereby granted, free of charge, to any person obtaining a copy
    of this software and associated documentation files (the "Software"), to deal
    in the Software without restriction, including without limitation the rights
    to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
    copies of the Software, and to permit persons to whom the Software is
    furnished to do so, subject to the following conditions:
-   
+
    The above copyright notice and this permission notice shall be included in
    all copies or substantial portions of the Software.
-   
+
    THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
    IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
    FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
@@ -35,36 +35,27 @@
 #include <htslib/vcf.h>
 #include <htslib/synced_bcf_reader.h>
 #include "bcftools.h"
+#include "peakfit.h"
 
 typedef struct
 {
-    int nvals;      // number of data points to fit against (excluding RR,AA peaks)
-    double *xvals;  // xvalues, pointer to dist_t.xvals
-    double *yvals;  // yvalues, pointer to dist_t.yvals
-    int ngauss;     // number of gaussian functions
-}
-data_t;
-
-typedef struct
-{
-    data_t dat;
     int nvals;          // all values, including RR,AA peaks
     double *xvals;      // pointer to args_t.xvals
-    double *yvals;   
+    double *yvals;
     int copy_number;    // heuristics to skip futile CN1 fits when no het peak is detected
-    int irr, iaa;       // chop off RR and AA peaks
+    int irr, ira, iaa;  // chop off RR and AA peaks
     char *chr;
 }
 dist_t;
 
 typedef struct
 {
-    int ndist, nbins;
+    int ndist, nbins, ra_rr_scaling, smooth;
     double *xvals;
     dist_t *dist;
     char **argv, *output_dir;
-    double fit_th, peak_symmetry, cn_penalty;
-    int argc, plot, verbose, regions_is_file, targets_is_file;
+    double fit_th, peak_symmetry, cn_penalty, min_peak_size, min_fraction;
+    int argc, plot, verbose, regions_is_file, targets_is_file, include_aa, force_cn;
     char *dat_fname, *fname, *regions_list, *targets_list, *sample;
     FILE *dat_fp;
 }
@@ -72,31 +63,56 @@ args_t;
 
 FILE *open_file(char **fname, const char *mode, const char *fmt, ...);
 
-static void init_dist(dist_t *dist, int verbose)
+static void init_dist(args_t *args, dist_t *dist, int verbose)
 {
     // isolate RR and AA peaks and rescale so that they are comparable to hets
     int i, irr, iaa, n = dist->nvals;
 
-    // smooth the distribution
+    // smooth the distribution, this is just to find the peaks
     double *tmp = (double*) malloc(sizeof(double)*n);
-    int win = 0.02*n < 1 ? 1 : 0.02*n;
-    double avg = 0;
-    for (i=0; i<win; i++) avg += dist->yvals[i];
-    for (i=0; i<n-win; i++)
+    int win  = args->smooth ? fabs(args->smooth)*2 + 1 : 7;   // must be an odd number
+    int hwin = win/2;
+    double avg = tmp[0] = dist->yvals[0];
+    for (i=1; i<hwin; i++)
+    {
+        avg += dist->yvals[2*i-1]; 
+        tmp[i] = avg/(2*i+1);
+    }
+    avg = 0;
+    for (i=0; i<n; i++)
+    {
+        avg += dist->yvals[i];
+        if ( i>=win-1 )
+        {
+            tmp[i-hwin] = avg/win;
+            avg -= dist->yvals[i-win+1];
+        }
+    }
+    for (i=n-hwin; i<n; i++)
     {
-        tmp[i] = avg / win;
-        avg += -dist->yvals[i] + dist->yvals[i+win];
+        avg -= dist->yvals[i-hwin];
+        hwin--;
+        tmp[i] = avg/(2*hwin+1);
+        avg -= dist->yvals[i-hwin];
     }
-    for (; i<n; i++) tmp[i] = avg;
 
     // find the extremes; first a simple approach: find a gap
     for (irr=0,i=0; i<n/2; i++) if ( tmp[i] < tmp[irr] ) irr = i;
     for (iaa=n-1,i=n-1; i>=n/2; i--) if ( tmp[i] < tmp[iaa] ) iaa = i;
     irr += win*0.5;
     iaa += win*0.5;
+    if ( iaa>=n ) iaa = n-1;
     if ( irr>=iaa ) error("FIXME: oops, dist normalization failed for %s: %d vs %d\n", dist->chr,irr,iaa); // we may need to be smarter
+    if ( args->smooth>0 ) for (i=0; i<n; i++) dist->yvals[i] = tmp[i];
     free(tmp);
 
+    // clean the data: the AA peak is occasionally not centered at 1.0 but is closer to the center, chop off
+    int imax_aa = iaa;
+    for (i=iaa; i<n; i++)
+        if ( dist->yvals[imax_aa] < dist->yvals[i] ) imax_aa = i;
+    dist->nvals = imax_aa+1;
+    if ( iaa>=dist->nvals ) iaa = dist->nvals-1;
+
     // find the maximum and scale the peaks (first draft: no attempt to join the segments smootly)
     double max_rr = 0, max_aa = 0, max_ra = 0, srr = 0, saa = 0, sra = 0;
     for (i=0; i<irr; i++)
@@ -123,7 +139,8 @@ static void init_dist(dist_t *dist, int verbose)
     //  Y:  cn=0     ra/rr=0.008316      aa/ra=7.250000      nra=12
     //  MT: cn=0     ra/rr=0.013699      aa/ra=0.666667      nra=3
 
-    if ( !sra || (sra/srr<0.1 && saa/sra>1.0) )
+    if ( !args->ra_rr_scaling ) max_ra = max_aa = max_rr;
+    if ( !sra || (sra/srr<0.1 && saa/sra>1.0) ) // too few hets, CN1
     {
         max_ra = max_aa;
         dist->copy_number = 1;
@@ -137,12 +154,14 @@ static void init_dist(dist_t *dist, int verbose)
     if ( max_ra ) for (i=irr; i<=iaa; i++) dist->yvals[i] /= max_ra;
     if ( max_aa ) for (i=iaa+1; i<n; i++) dist->yvals[i] /= max_aa;
 
-    dist->dat.yvals = &dist->yvals[irr];
-    dist->dat.xvals = &dist->xvals[irr];
-    dist->dat.nvals = iaa - irr + 1;
+    dist->irr = irr;
+    dist->iaa = iaa;
+    dist->ira = n*0.5;
 
     if ( verbose )
-        fprintf(stderr,"%s:\t cn=%2d \t ra/rr=%f \t aa/ra=%f \t nra=%d\n", dist->chr,dist->copy_number,sra/srr,saa/sra, (int)sra);
+        fprintf(stderr,"%s:\t irr,ira,iaa=%.2f,%.2f,%.2f \t cn=%2d \t ra/rr=%f \t aa/ra=%f \t nra=%d\n", 
+            dist->chr, dist->xvals[irr],dist->xvals[dist->ira],dist->xvals[iaa],
+            dist->copy_number,sra/srr,saa/sra, (int)sra);
 }
 
 static void init_data(args_t *args)
@@ -208,7 +227,17 @@ static void init_data(args_t *args)
     bcf_sr_destroy(files);
 
     for (idist=0; idist<args->ndist; idist++)
-        init_dist(&args->dist[idist],args->verbose);
+    {
+        #if 0
+            int j;
+            for (j=0; j<args->nbins; j++)
+            {
+                double x = args->dist[idist].xvals[j];
+                args->dist[idist].yvals[j] = exp(-(x-0.5)*(x-0.5)/1e-3);
+            }
+        #endif
+        init_dist(args, &args->dist[idist],args->verbose);
+    }
 
     args->dat_fp = open_file(&args->dat_fname,"w","%s/dist.dat", args->output_dir);
     fprintf(args->dat_fp, "# This file was produced by: bcftools polysomy(%s+htslib-%s), the command line was:\n", bcftools_version(),hts_version());
@@ -217,7 +246,7 @@ static void init_data(args_t *args)
         fprintf(args->dat_fp, " %s",args->argv[i]);
     fprintf(args->dat_fp,"\n#\n");
     fprintf(args->dat_fp,"# DIST\t[2]Chrom\t[3]BAF\t[4]Normalized Count\n");
-    fprintf(args->dat_fp,"# FIT\t[2]Chrom\t[3]Mean of fitted Gaussian\t[4]Scale\t[5]Sigma[6]\tMean etc.\n");
+    fprintf(args->dat_fp,"# FIT\t[2]Goodness of Fit\t[3]iFrom\t[4]iTo\t[5]The Fitted Function\n");
     fprintf(args->dat_fp,"# CN\t[2]Chrom\t[3]Estimated Copy Number\t[4]Absolute fit deviation\n");
 
     char *fname = NULL;
@@ -229,7 +258,8 @@ static void init_data(args_t *args)
         "import matplotlib as mpl\n"
         "mpl.use('Agg')\n"
         "import matplotlib.pyplot as plt\n"
-        "import csv,math,sys,argparse\n"
+        "import csv,sys,argparse\n"
+        "from math import exp\n"
         "\n"
         "outdir = '%s'\n"
         "\n"
@@ -246,27 +276,25 @@ static void init_data(args_t *args)
         "              dat[chr].append(row)\n"
         "          elif type=='FIT':\n"
         "              if chr not in fit: fit[chr] = []\n"
-        "              fit[chr] = row[2:]\n"
+        "              fit[chr].append(row)\n"
         "          elif type=='CN':\n"
         "              cn[chr] = row[2]\n"
         "\n"
-        "def fitted_func(xvals,params):\n"
-        "   n = len(params)/3\n"
-        "   out = []\n"
-        "   for x in xvals:\n"
-        "       y = 0\n"
-        "       for i in range(n):\n"
-        "           mean  = float(params[i*3+0])\n"
-        "           scale = float(params[i*3+1])\n"
-        "           sigma = float(params[i*3+2])\n"
-        "           y += scale * math.exp(-(float(x)-mean)**2/sigma**2)\n"
-        "       out.append(y)\n"
-        "   return out\n"
-        "\n"
         "def plot_dist(dat,fit,chr):\n"
         "   fig, ax = plt.subplots(1, 1, figsize=(7,5))\n"
-        "   ax.plot([x[2] for x in dat[chr]],[x[3] for x in dat[chr]],'-',label='Distribution')\n"
-        "   ax.plot([x[2] for x in dat[chr]],fitted_func([x[2] for x in dat[chr]], fit[chr]),'-',label='Best Fit')\n"
+        "   ax.plot([x[2] for x in dat[chr]],[x[3] for x in dat[chr]],'k-',label='Distribution')\n"
+        "   if chr in fit:\n"
+        "       for i in range(len(fit[chr])):\n"
+        "           pfit = fit[chr][i]\n"
+        "           exec('def xfit(x): return '+pfit[5])\n"
+        "           istart = int(pfit[3])\n"
+        "           iend   = int(pfit[4])+1\n"
+        "           vals   = dat[chr][istart:iend]\n"
+        "           args   = {}\n"
+        "           if i==0: args = {'label':'Target to Fit'}\n"
+        "           ax.plot([x[2] for x in vals],[x[3] for x in vals],'r-',**args)\n"
+        "           if i==0: args = {'label':'Best Fit'}\n"
+        "           ax.plot([x[2] for x in vals],[xfit(float(x[2])) for x in vals],'g-',**args)\n"
         "   ax.set_title('BAF distribution, chr'+chr)\n"
         "   ax.set_xlabel('BAF')\n"
         "   ax.set_ylabel('Frequency')\n"
@@ -293,13 +321,18 @@ static void init_data(args_t *args)
         "   plt.savefig(outdir+'/copy-number.png')\n"
         "   plt.close()\n"
         "\n"
+        "class myParser(argparse.ArgumentParser):\n"
+        "   def error(self, message):\n"
+        "       self.print_help()\n"
+        "       sys.stderr.write('error: %%s\\n' %% message)\n"
+        "       sys.exit(2)\n"
+        "\n"
         "def main():\n"
-        "   parser = argparse.ArgumentParser()\n"
+        "   parser = myParser()\n"
         "   parser.add_argument('-a', '--all', action='store_true', help='Create all plots')\n"
         "   parser.add_argument('-c', '--copy-number', action='store_true', help='Create copy-number plot')\n"
         "   parser.add_argument('-d', '--distrib', metavar='CHR', help='Plot BAF distribution of a single chromosome')\n"
         "   args = parser.parse_args()\n"
-        "   if args.distrib==None and not args.all and not args.copy_number: parser.print_help()\n"
         "   dat = {}; fit = {}; cn = {}\n"
         "   read_dat(dat,fit,cn)\n"
         "   if args.distrib!=None:\n"
@@ -309,6 +342,8 @@ static void init_data(args_t *args)
         "       plot_copy_number(cn)\n"
         "   elif args.copy_number:\n"
         "       plot_copy_number(cn)\n"
+        "   else:\n"
+        "       for chr in dat: plot_dist(dat,fit,chr)\n"
         "\n"
         "if __name__ == '__main__':\n"
         "   main()\n",
@@ -333,253 +368,251 @@ static void destroy_data(args_t *args)
     fclose(args->dat_fp);
 }
 
-static void save_dist(args_t *args, int idist, int ngauss, double *params)
+static void save_dist(args_t *args, dist_t *dist)
 {
     int i;
     for (i=0; i<args->nbins; i++)
-        fprintf(args->dat_fp,"DIST\t%s\t%f\t%f\n",args->dist[idist].chr,args->dist[idist].xvals[i],args->dist[idist].yvals[i]);
-    fprintf(args->dat_fp,"FIT\t%s", args->dist[idist].chr);
-    for (i=0; i<ngauss*3; i++) fprintf(args->dat_fp,"\t%f", params[i]);
-    fprintf(args->dat_fp,"\n");
+        fprintf(args->dat_fp,"DIST\t%s\t%f\t%f\n",dist->chr,dist->xvals[i],dist->yvals[i]);
 }
-
-int func_f(const gsl_vector *params, void *data, gsl_vector *yvals)
+static void fit_curves(args_t *args)
 {
-    data_t *dat = (data_t *) data;
+    peakfit_t *pkf = peakfit_init();
+    peakfit_verbose(pkf,args->verbose);
 
-    int i, j;
-    for (i=0; i<dat->nvals; i++)
+    int i, nmc = 50;
+    for (i=0; i<args->ndist; i++)
     {
-        double xi = dat->xvals[i];
-        double yi = 0;
-        for (j=0; j<dat->ngauss; j++)
-        {
-            double center = gsl_vector_get(params,j*3 + 0);
-            double scale  = gsl_vector_get(params,j*3 + 1);
-            double sigma  = gsl_vector_get(params,j*3 + 2);
+        dist_t *dist = &args->dist[i];
+        save_dist(args, &args->dist[i]);
 
-            double zi = (xi - center) / sigma;
-            yi += scale*scale * exp(-zi*zi);
+        if ( dist->copy_number!=0 )
+        {
+            fprintf(args->dat_fp,"CN\t%s\t%.2f\n", dist->chr,(float)dist->copy_number);
+            continue;
         }
-        gsl_vector_set(yvals, i, (yi - dat->yvals[i])/0.1);
-    }
-    return GSL_SUCCESS;
-}
-
-int func_df(const gsl_vector *params, void *data, gsl_matrix *jacobian)
-{
-    data_t *dat = (data_t *) data;
 
-    int i, j;
-    for (i=0; i<dat->nvals; i++)
-    {
-        // Jacobian matrix J(i,j) = dfi / dxj,
-        // where fi = (Yi - yi),
-        //       Yi = scale^2 * exp(-(center - xi)^2/sigma^2)
-        //
-
-        double xi = dat->xvals[i];
-        for (j=0; j<dat->ngauss; j++)
+        if ( args->verbose )
+            fprintf(stderr,"%s:\n", dist->chr);
+
+        int nrr_aa  = dist->iaa - dist->irr + 1;
+        int nrr_ra  = dist->ira - dist->irr + 1;
+        int naa_max = dist->nvals - dist->iaa;
+        double xrr  = dist->xvals[dist->irr], *xrr_vals = &dist->xvals[dist->irr], *yrr_vals = &dist->yvals[dist->irr];
+        double xaa  = dist->xvals[dist->iaa], *xaa_vals = &dist->xvals[dist->iaa], *yaa_vals = &dist->yvals[dist->iaa];
+        double xra  = dist->xvals[dist->ira];
+        double xmax = dist->xvals[dist->nvals-1];
+
+
+        // CN2
+        double cn2aa_fit = 0, cn2ra_fit, cn2_fit;
+        char *cn2aa_func = 0, *cn2ra_func;
+        double cn2aa_params[3] = {1,1,1} ,cn2ra_params[3];
+        if ( args->include_aa )
         {
-            double center = gsl_vector_get(params,j*3 + 0);
-            double scale  = gsl_vector_get(params,j*3 + 1);
-            double sigma  = gsl_vector_get(params,j*3 + 2);
-
-            double zi = (xi - center) / sigma;
-            double ei = exp(-zi*zi);
-
-            gsl_matrix_set(jacobian, i, j*3 + 0, 2*scale*scale*(xi-center)/(sigma*sigma)*ei);
-            gsl_matrix_set(jacobian, i, j*3 + 1, 2*scale*ei);
-            gsl_matrix_set(jacobian, i, j*3 + 2, 2*scale*scale*(xi-center)*(xi-center)/(sigma*sigma*sigma)*ei);
+            peakfit_reset(pkf);
+            peakfit_add_exp(pkf, 1.0,1.0,0.2, 5);
+            peakfit_set_mc(pkf, 0.01,0.3,2,nmc);
+            peakfit_set_mc(pkf, 0.05,1.0,0,nmc);
+            cn2aa_fit  = peakfit_run(pkf, naa_max, xaa_vals, yaa_vals);
+            cn2aa_func = strdup(peakfit_sprint_func(pkf));
+            peakfit_get_params(pkf,0,cn2aa_params,3);
         }
-    }
-    return GSL_SUCCESS;
-}
-
-int func_set(const gsl_vector *params, void *data, gsl_vector *yvals, gsl_matrix *jacobian)
-{
-    func_f(params, data, yvals);
-    func_df(params, data, jacobian);
-    return GSL_SUCCESS;
-}
-static double eval_fit(int nvals, double *xvals, double *yvals, int ngauss, double *params)
-{
-    double sum = 0;
-    int i, j;
-    for (i=0; i<nvals; i++)
-    {
-        double yval = 0;
-        for (j=0; j<ngauss; j++)
+        peakfit_reset(pkf);
+        peakfit_add_bounded_gaussian(pkf, 1.0,0.5,0.03, 0.45,0.55, 7);
+        peakfit_set_mc(pkf, 0.01,0.3,2,nmc);
+        peakfit_set_mc(pkf, 0.05,1.0,0,nmc);
+        cn2ra_fit  = peakfit_run(pkf, nrr_aa,xrr_vals,yrr_vals);
+        cn2ra_func = strdup(peakfit_sprint_func(pkf));
+        cn2_fit    = cn2ra_fit + cn2aa_fit;
+        peakfit_get_params(pkf,0,cn2ra_params,3);
+
+
+        // CN3: fit two peaks, then enforce the symmetry and fit again
+        double cn3rra_params[5], cn3raa_params[5], *cn3aa_params = cn2aa_params;
+        double cn3aa_fit = cn2aa_fit, cn3ra_fit;
+        char *cn3aa_func = cn2aa_func, *cn3ra_func;
+        double min_dx3   = 0.5 - 1./(args->min_fraction+2);
+        peakfit_reset(pkf);
+        peakfit_add_bounded_gaussian(pkf, 1.0,1/3.,0.03, xrr,xra-min_dx3, 7);
+        peakfit_set_mc(pkf, xrr,xra-min_dx3, 1,nmc);
+        peakfit_add_bounded_gaussian(pkf, 1.0,2/3.,0.03, xra+min_dx3,xaa, 7);
+        peakfit_set_mc(pkf, xra+min_dx3,xaa, 1,nmc);
+        peakfit_run(pkf, nrr_aa, xrr_vals, yrr_vals);
+        // force symmetry around x=0.5
+        peakfit_get_params(pkf,0,cn3rra_params,5);
+        peakfit_get_params(pkf,1,cn3raa_params,5);
+        double cn3_dx = (0.5-cn3rra_params[1] + cn3raa_params[1]-0.5)*0.5;
+        if ( cn3_dx > 0.5/3 ) cn3_dx = 0.5/3;   // CN3 peaks should not be separated by more than 1/3
+        peakfit_reset(pkf);
+        peakfit_add_gaussian(pkf, cn3rra_params[0],0.5-cn3_dx,cn3rra_params[2], 5);
+        peakfit_add_gaussian(pkf, cn3raa_params[0],0.5+cn3_dx,cn3raa_params[2], 5);
+        cn3ra_fit  = peakfit_run(pkf, nrr_aa, xrr_vals, yrr_vals);
+        cn3ra_func = strdup(peakfit_sprint_func(pkf));
+        // compare peak sizes
+        peakfit_get_params(pkf,0,cn3rra_params,3);
+        peakfit_get_params(pkf,1,cn3raa_params,3);
+        double cn3rra_size = cn3rra_params[0]*cn3rra_params[0];
+        double cn3raa_size = cn3raa_params[0]*cn3raa_params[0];
+        double cn3_dy      = cn3rra_size > cn3raa_size ? cn3raa_size/cn3rra_size : cn3rra_size/cn3raa_size;
+        double cn3_frac    = (1 - 2*cn3rra_params[1]) / cn3rra_params[1];
+        double cn3_fit     = cn3ra_fit + cn3aa_fit;
+        // A very reasonable heuristics: check if the peak's width converged, exclude far too broad or far too narrow peaks
+        if ( cn3rra_params[2]>0.3  || cn3raa_params[2]>0.3 ) cn3_fit = HUGE_VAL;
+        if ( cn3rra_params[2]<1e-2 || cn3raa_params[2]<1e-2 ) cn3_fit = HUGE_VAL;
+
+
+        // CN4 (contaminations)
+        // - first fit only the [0,0.5] part of the data, then enforce the symmetry and fit again
+        // - min_frac=1 (resp. 0.5) is interpreted as 50:50% (rep. 75:25%) contamination
+        double cn4AAaa_params[3] = {1,1,1} ,cn4AAra_params[3] = {1,1,1}, cn4RAra_params[3], cn4RArr_params[5], cn4RAaa_params[5];
+        double cn4aa_fit = 0, cn4ra_fit;
+        char *cn4aa_func = 0, *cn4ra_func;
+        double min_dx4   = 0.25*args->min_fraction;
+        if ( args->include_aa )
         {
-            double center = params[j*3 + 0];
-            double scale  = params[j*3 + 1];
-            double sigma  = params[j*3 + 2];
-            
-            double zi = (xvals[i] - center) / sigma;
-            yval += scale * exp(-zi*zi);
+            peakfit_reset(pkf);
+            peakfit_add_exp(pkf, 0.5,1.0,0.2, 5);
+            peakfit_set_mc(pkf, 0.01,0.3,2,nmc);
+            peakfit_add_bounded_gaussian(pkf, 0.4,(xaa+xmax)*0.5,2e-2, xaa,xmax, 7);
+            peakfit_set_mc(pkf, xaa,xmax, 1,nmc);
+            cn4aa_fit  = peakfit_run(pkf, naa_max, xaa_vals,yaa_vals);
+            cn4aa_func = strdup(peakfit_sprint_func(pkf));
+            peakfit_get_params(pkf,0,cn4AAaa_params,3);
+            peakfit_get_params(pkf,1,cn4AAra_params,5);
         }
-        sum += fabs(yval - yvals[i]);
-    }
-    return sum;
-}
-
-static int gauss_fit(dist_t *dist, int ngauss, double *params)
-{
-    data_t *dat = &dist->dat;
-    dat->ngauss = ngauss;
-
-    gsl_multifit_function_fdf mfunc;
-    mfunc.f   = &func_f;
-    mfunc.df  = &func_df;
-    mfunc.fdf = &func_set;
-    mfunc.n   = dat->nvals;
-    mfunc.p   = ngauss*3;      // number of fitting parameters
-    mfunc.params = dat;
-
-    const gsl_multifit_fdfsolver_type *solver_type;
-    gsl_multifit_fdfsolver *solver;
-    gsl_vector_view vview = gsl_vector_view_array(params, mfunc.p);
-    solver_type = gsl_multifit_fdfsolver_lmsder;
-    solver = gsl_multifit_fdfsolver_alloc(solver_type, dat->nvals, mfunc.p);
-    gsl_multifit_fdfsolver_set(solver, &mfunc, &vview.vector);
-
-    int i, status;
-    size_t iter = 0;
-    do
-    {
-        status = gsl_multifit_fdfsolver_iterate(solver);
-        if ( status ) break;
-        status = gsl_multifit_test_delta(solver->dx, solver->x, 1e-4, 1e-4);
-    }
-    while (status == GSL_CONTINUE && iter++ < 500);
-
-    for (i=0; i<mfunc.p; i++)
-        params[i] = gsl_vector_get(solver->x, i);
-
-    gsl_multifit_fdfsolver_free(solver);
-    return iter>500 ? -1 : 0;
-}
-
-static double best_fit(args_t *args, dist_t *dist, int ngauss, double *params)
-{
-    if ( ngauss==1 )
-    {
-        gauss_fit(dist,ngauss,params);
-        params[1] *= params[1];
-        return eval_fit(dist->dat.nvals, dist->dat.xvals, dist->dat.yvals, ngauss,params);
-    }
-
-    int i, j, n = 3;
-    int ipk = 3*(ngauss-1);
-    double delta = 0.5 * (params[ipk] - params[0]) / n;
-    double best_params[9], tmp_params[9], best_fit = HUGE_VAL;
-    for (i=0; i<n; i++)
-    {
-        memcpy(tmp_params,params,sizeof(double)*ngauss*3);
-        tmp_params[0]   += delta*i;
-        tmp_params[ipk] -= delta*i;
-        if ( gauss_fit(dist,ngauss,tmp_params)<0 ) continue;    // did not converge
-
-        for (j=0; j<ngauss; j++) tmp_params[j*3+1] *= tmp_params[j*3+1];
-
-        // From the nature of the data, we can assume that in presence of
-        // multiple peaks they will be placed symmetrically around 0.5. Also
-        // their size should be about the same. We evaluate the fit with this
-        // in mind.
-        double dx = fabs(0.5 - tmp_params[0]) + fabs(tmp_params[ipk] - 0.5);
-        tmp_params[0] = 0.5 - dx*0.5;
-        tmp_params[ipk] = 0.5 + dx*0.5;
-        double fit = eval_fit(dist->dat.nvals, dist->dat.xvals, dist->dat.yvals, ngauss, tmp_params);
-
-        if ( best_fit < fit ) continue;     // worse than previous
-        best_fit = fit;
-        memcpy(best_params,tmp_params,sizeof(double)*ngauss*3);
-    }
-    memcpy(params,best_params,sizeof(double)*ngauss*3);
-    return best_fit;
-}
-
-static void print_params(data_t *dat, int ngauss, double *params, float fit, float frac, char fail, char comment)
-{
-    int i, j;
-    printf("\t%c%c fit=%f frac=%.2f .. center,scale,sigma = ", comment,fail?fail:'o',fit,frac);
-    for (i=0; i<ngauss; i++)
-    {
-        if ( i!=0 ) printf("\t");
-        for (j=0; j<3; j++) printf(" %f", params[i*3+j]);
-    }
-    printf("\n");
-}
-static void fit_curves(args_t *args)
-{
-    int i;
-    for (i=0; i<args->ndist; i++)
-    {
-        dist_t *dist = &args->dist[i];
-        if ( dist->copy_number!=0 )
+        peakfit_reset(pkf);
+        // first fit only the [0,0.5] part of the data
+        peakfit_add_gaussian(pkf, 1.0,0.5,0.03, 5);
+        peakfit_add_bounded_gaussian(pkf, 0.6,0.3,0.03, xrr,xra-min_dx4, 7);
+        peakfit_set_mc(pkf, xrr,xra-min_dx4,2,nmc);
+        peakfit_run(pkf, nrr_ra , xrr_vals, yrr_vals);
+        // now forcet symmetry around x=0.5
+        peakfit_get_params(pkf,0,cn4RAra_params,3);
+        peakfit_get_params(pkf,1,cn4RArr_params,5);
+        double cn4_dx = 0.5-cn4RArr_params[1];
+        if ( cn4_dx > 0.25 ) cn4_dx = 0.25;   // CN4 peaks should not be separated by more than 0.5
+        peakfit_reset(pkf);
+        peakfit_add_gaussian(pkf, cn4RAra_params[0],0.5,cn4RAra_params[2], 5);
+        peakfit_add_gaussian(pkf, cn4RArr_params[0],0.5-cn4_dx,cn4RArr_params[2], 5);
+        peakfit_add_gaussian(pkf, cn4RArr_params[0],0.5+cn4_dx,cn4RArr_params[2], 5);
+        peakfit_set_mc(pkf, 0.1,cn4RAra_params[0],0,nmc);
+        peakfit_set_mc(pkf, 0.01,0.1,2,nmc);
+        cn4ra_fit  = peakfit_run(pkf, nrr_aa , xrr_vals, yrr_vals);
+        cn4ra_func = strdup(peakfit_sprint_func(pkf));
+        peakfit_get_params(pkf,0,cn4RAra_params,3);
+        peakfit_get_params(pkf,1,cn4RArr_params,3);
+        peakfit_get_params(pkf,2,cn4RAaa_params,3);
+        double cn4RAra_size = cn4RAra_params[0]==0 ? HUGE_VAL : cn4RAra_params[0]*cn4RAra_params[0];
+        double cn4RArr_size = cn4RArr_params[0]*cn4RArr_params[0];
+        double cn4RAaa_size = cn4RAaa_params[0]*cn4RAaa_params[0];
+        double cn4RArr_dy   = cn4RArr_size < cn4RAra_size ? cn4RArr_size/cn4RAra_size : cn4RAra_size/cn4RArr_size;
+        double cn4RAaa_dy   = cn4RAaa_size < cn4RAra_size ? cn4RAaa_size/cn4RAra_size : cn4RAra_size/cn4RAaa_size;
+        double cn4_dy       = cn4RArr_dy < cn4RAaa_dy ? cn4RArr_dy/cn4RAaa_dy : cn4RAaa_dy/cn4RArr_dy;
+        double cn4_ymin     = cn4RArr_size < cn4RAaa_size ? cn4RArr_size/cn4RAra_size : cn4RAaa_size/cn4RAra_size;
+        cn4_dx              = (cn4RAaa_params[1]-0.5) - (0.5-cn4RArr_params[1]);
+        double cn4_frac     = cn4RAaa_params[1] - cn4RArr_params[1];
+        double cn4_fit      = cn4ra_fit + cn4aa_fit;
+        // A very reasonable heuristics: check if the peak's width converged, exclude far too broad or far too narrow peaks
+        if ( cn4RAra_params[2]>0.3 || cn4RArr_params[2]>0.3 || cn4RAaa_params[2]>0.3 ) cn4_fit = HUGE_VAL;
+        if ( cn4RAra_params[2]<1e-2 || cn4RArr_params[2]<1e-2 || cn4RAaa_params[2]<1e-2 ) cn4_fit = HUGE_VAL;
+
+
+        // Choose the best match
+        char cn2_fail = '*', cn3_fail = '*', cn4_fail = '*';
+        if ( cn2_fit > args->fit_th ) cn2_fail = 'f';
+
+        if ( cn3_fit > args->fit_th ) cn3_fail = 'f';
+        else if ( cn3_dy < args->peak_symmetry ) cn3_fail = 'y';    // size difference is too big
+
+        if ( cn4_fit > args->fit_th ) cn4_fail = 'f';
+        else if ( cn4_ymin < args->min_peak_size ) cn4_fail = 'y';      // side peak is too small
+        else if ( cn4_dy < args->peak_symmetry ) cn4_fail = 'Y';    // size difference is too big
+        else if ( cn4_dx > 0.1 ) cn4_fail = 'x';                    // side peaks placed assymetrically
+
+        double cn = -1, fit = cn2_fit;
+        if ( cn2_fail == '*' ) { cn = 2; fit = cn2_fit; }
+        if ( cn3_fail == '*' )
         {
-            fprintf(args->dat_fp,"CN\t%s\t%.2f\n", dist->chr,(float)dist->copy_number);
-            save_dist(args, i, 0, NULL);
-            continue;
+            // Use cn_penalty as a tiebreaker. If set to 0.3, cn3_fit must be 30% smaller than cn2_fit.
+            if ( cn<0 || cn3_fit < (1-args->cn_penalty) * fit )
+            {
+                cn = 2 + cn3_frac; 
+                fit = cn3_fit; 
+                if ( cn2_fail=='*' ) cn2_fail = 'p';
+            }
+            else cn3_fail = 'p';
+        }
+        if ( cn4_fail == '*' )
+        {
+            if ( cn<0 || cn4_fit < (1-args->cn_penalty) * fit )
+            {
+                cn = 3 + cn4_frac;
+                fit = cn4_fit;
+                if ( cn2_fail=='*' ) cn2_fail = 'p';
+                if ( cn3_fail=='*' ) cn3_fail = 'p';
+            }
+            else cn4_fail = 'p';
         }
-
-        // Parameters (center,scale,sigma) for gaussian peaks.
-        double params_cn2[] = { 1/2.,0.5,0.05 };
-        double params_cn3[] = { 1/3.,0.5,0.05, 2/3.,0.5,0.05 };
-        double params_cn4[] = { 1/4.,0.5,0.05, 1/2.,0.5,0.05, 3/4.,0.5,0.05 };
-
-        double fit_cn2 = best_fit(args,&args->dist[i],1,params_cn2);
-        double fit_cn3 = best_fit(args,&args->dist[i],2,params_cn3);
-        double fit_cn4 = best_fit(args,&args->dist[i],3,params_cn4);
-
-        double dx_cn3  = fabs(params_cn3[0] - params_cn3[3]);
-        double dx_cn4  = fabs(params_cn4[0] - params_cn4[6]);
-        double dy_cn3  = params_cn3[1] > params_cn3[4] ? params_cn3[4]/params_cn3[1] : params_cn3[1]/params_cn3[4];
-        double dy_cn4a = params_cn4[1] > params_cn4[7] ? params_cn4[7]/params_cn4[1] : params_cn4[1]/params_cn4[7]; // side peaks
-        double ymax = params_cn4[1] > params_cn4[7] ? params_cn4[1] : params_cn4[7];
-        double dy_cn4b = ymax > params_cn4[4] ? params_cn4[4]/ymax : ymax/params_cn4[4];    // middle peak
-
-        // Three peaks (CN4) are always a better fit than two (CN3) or one (CN2). Therefore
-        // check that peaks are well separated and that the peak sizes are reasonable
-        char cn2_fail = 0, cn3_fail = 0, cn4_fail = 0;
-        if ( fit_cn2 > args->fit_th ) cn2_fail = 'f';
-
-        if ( fit_cn3 > args->fit_th ) cn3_fail = 'f';
-        else if ( dx_cn3 < 0.05 ) cn3_fail = 'x';         // peak separation: at least ~10% of cells
-        else if ( dy_cn3 < args->peak_symmetry ) cn3_fail = 'y';    
-
-        if ( fit_cn4 > args->fit_th ) cn4_fail = 'f';
-        else if ( dx_cn4 < 0.1 ) cn4_fail = 'x';            // peak separation
-        else if ( dy_cn4a < args->peak_symmetry ) cn4_fail = 'y';
-        else if ( dy_cn4b < args->peak_symmetry ) cn4_fail = 'Y';
-
-        // Estimate fraction of affected cells. For CN4 we estimate
-        // contamination (the fraction of foreign cells), which is more
-        // common than CN4; hence the value is from the interval [0,0.5].
-        //      CN3 .. f = 2*dx/(1-dx)
-        //      CN4 .. f = dx
-        dx_cn3 = 2*dx_cn3 / (1-dx_cn3);
-
-        double cn = -1, fit = fit_cn2;
-        if ( !cn2_fail ) { cn = 2; fit = fit_cn2; }
-        if ( !cn3_fail && fit_cn3 < args->cn_penalty * fit ) { cn = 3; fit = fit_cn3; }
-        if ( !cn4_fail && fit_cn4 < args->cn_penalty * fit ) { cn = 4; fit = fit_cn4; }
-
-        if ( cn==-1 ) save_dist(args, i, 0, NULL);
-        else if ( cn==2 ) save_dist(args, i, 1, params_cn2);
-        else if ( cn==3 ) { save_dist(args, i, 2, params_cn3); cn = 2 + dx_cn3; }
-        else if ( cn==4 ) { save_dist(args, i, 3, params_cn4); cn = 3 + dx_cn4; }
 
         if ( args->verbose )
         {
-            printf("%s: \n", args->dist[i].chr);
-            print_params(&args->dist[i].dat, 1, params_cn2, fit_cn2, 1.0,    cn2_fail, cn==2 ? '*' : ' ');
-            print_params(&args->dist[i].dat, 2, params_cn3, fit_cn3, dx_cn3, cn3_fail, cn>2 && cn<=3 ? '*' : ' ');
-            print_params(&args->dist[i].dat, 3, params_cn4, fit_cn4, dx_cn4, cn4_fail, cn>3 ? '*' : ' ');
-            printf("\n");
+            fprintf(stderr,"\tcn2 %c fit=%e\n", cn2_fail, cn2_fit);
+            fprintf(stderr,"\t       .. %e\n", cn2ra_fit);
+            fprintf(stderr,"\t            RA:   %f %f %f\n", cn2ra_params[0],cn2ra_params[1],cn2ra_params[2]);
+            fprintf(stderr,"\t       .. %e\n", cn2aa_fit);
+            fprintf(stderr,"\t            AA:   %f %f %f\n", cn2aa_params[0],cn2aa_params[1],cn2aa_params[2]);
+            fprintf(stderr,"\t      func:\n");
+            fprintf(stderr,"\t            %s\n", cn2ra_func);
+            fprintf(stderr,"\t            %s\n", cn2aa_func);
+            fprintf(stderr,"\n");
+            fprintf(stderr,"\tcn3 %c fit=%e  frac=%f  symmetry=%f\n", cn3_fail, cn3_fit, cn3_frac, cn3_dy);
+            fprintf(stderr,"\t       .. %e\n", cn3ra_fit);
+            fprintf(stderr,"\t            RRA:  %f %f %f\n", cn3rra_params[0],cn3rra_params[1],cn3rra_params[2]);
+            fprintf(stderr,"\t            RAA:  %f %f %f\n", cn3raa_params[0],cn3raa_params[1],cn3raa_params[2]);
+            fprintf(stderr,"\t       .. %e\n", cn3aa_fit);
+            fprintf(stderr,"\t            AAA:  %f %f %f\n", cn3aa_params[0],cn3aa_params[1],cn3aa_params[2]);
+            fprintf(stderr,"\t      func:\n");
+            fprintf(stderr,"\t            %s\n", cn3ra_func);
+            fprintf(stderr,"\t            %s\n", cn3aa_func);
+            fprintf(stderr,"\n");
+            fprintf(stderr,"\tcn4 %c fit=%e  frac=%f  symmetry=%f ymin=%f\n", cn4_fail, cn4_fit, cn4_frac, cn4_dy, cn4_ymin);
+            fprintf(stderr,"\t       .. %e\n", cn4ra_fit);
+            fprintf(stderr,"\t            RArr:  %f %f %f\n", cn4RArr_params[0],cn4RArr_params[1],cn4RArr_params[2]);
+            fprintf(stderr,"\t            RAra:  %f %f %f\n", cn4RAra_params[0],cn4RAra_params[1],cn4RAra_params[2]);
+            fprintf(stderr,"\t            RAaa:  %f %f %f\n", cn4RAaa_params[0],cn4RAaa_params[1],cn4RAaa_params[2]);
+            fprintf(stderr,"\t       .. %e\n", cn4aa_fit);
+            fprintf(stderr,"\t            AAaa:  %f %f %f\n", cn4AAaa_params[0],cn4AAaa_params[1],cn4AAaa_params[2]);
+            fprintf(stderr,"\t      func:\n");
+            fprintf(stderr,"\t            %s\n", cn4ra_func);
+            fprintf(stderr,"\t            %s\n", cn4aa_func);
+            fprintf(stderr,"\n");
+        }
+
+        if ( args->force_cn==2 || cn2_fail == '*' )
+        {
+            fprintf(args->dat_fp,"FIT\t%s\t%e\t%d\t%d\t%s\n", dist->chr,cn2ra_fit,dist->irr,dist->iaa,cn2ra_func);
+            if ( cn2aa_func ) fprintf(args->dat_fp,"FIT\t%s\t%e\t%d\t%d\t%s\n", dist->chr,cn2aa_fit,dist->iaa,dist->nvals-1,cn2aa_func);
+        }
+        if ( args->force_cn==3 || cn3_fail == '*' )
+        {
+            fprintf(args->dat_fp,"FIT\t%s\t%e\t%d\t%d\t%s\n", dist->chr,cn3ra_fit,dist->irr,dist->iaa,cn3ra_func);
+            if ( cn3aa_func ) fprintf(args->dat_fp,"FIT\t%s\t%e\t%d\t%d\t%s\n", dist->chr,cn3aa_fit,dist->iaa,dist->nvals-1,cn3aa_func);
+        }
+        if ( args->force_cn==4 || cn4_fail == '*' )
+        {
+            fprintf(args->dat_fp,"FIT\t%s\t%e\t%d\t%d\t%s\n", dist->chr,cn4ra_fit,dist->irr,dist->iaa,cn4ra_func);
+            if ( cn4aa_func ) fprintf(args->dat_fp,"FIT\t%s\t%e\t%d\t%d\t%s\n", dist->chr,cn4aa_fit,dist->iaa,dist->nvals-1,cn4aa_func);
         }
         fprintf(args->dat_fp,"CN\t%s\t%.2f\t%f\n", dist->chr, cn, fit);
+
+        free(cn2aa_func);
+        free(cn2ra_func);
+        free(cn3ra_func);
+        free(cn4ra_func);
+        free(cn4aa_func);
     }
+
+    peakfit_destroy(pkf);
 }
 
 static void usage(args_t *args)
@@ -587,6 +620,7 @@ static void usage(args_t *args)
     fprintf(stderr, "\n");
     fprintf(stderr, "About:   Detect number of chromosomal copies from Illumina's B-allele frequency (BAF)\n");
     fprintf(stderr, "Usage:   bcftools polysomy [OPTIONS] <file.vcf>\n");
+    fprintf(stderr, "\n");
     fprintf(stderr, "General options:\n");
     fprintf(stderr, "    -o, --output-dir <path>        \n");
     fprintf(stderr, "    -r, --regions <region>         restrict to comma-separated list of regions\n");
@@ -595,10 +629,14 @@ static void usage(args_t *args)
     fprintf(stderr, "    -t, --targets <region>         similar to -r but streams rather than index-jumps\n");
     fprintf(stderr, "    -T, --targets-file <file>      similar to -R but streams rather than index-jumps\n");
     fprintf(stderr, "    -v, --verbose                  \n");
+    fprintf(stderr, "\n");
     fprintf(stderr, "Algorithm options:\n");
-    fprintf(stderr, "    -c, --cn-penalty <float>       penalty for increasing CN (smaller more strict) [0.7]\n");
-    fprintf(stderr, "    -f, --fit-th <float>           goodness of fit threshold (smaller more strict) [3.0]\n");
-    fprintf(stderr, "    -p, --peak-symmetry <float>    peak symmetry threshold (bigger more strict) [0.7]\n");
+    fprintf(stderr, "    -b, --peak-size <float>        minimum peak size (0-1, larger is stricter) [0.1]\n");
+    fprintf(stderr, "    -c, --cn-penalty <float>       penalty for increasing CN (0-1, larger is stricter) [0.7]\n");
+    fprintf(stderr, "    -f, --fit-th <float>           goodness of fit threshold (>0, smaller is stricter) [3.3]\n");
+    fprintf(stderr, "    -i, --include-aa               include the AA peak in CN2 and CN3 evaluation\n");
+    fprintf(stderr, "    -m, --min-fraction <float>     minimum distinguishable fraction of aberrant cells [0.1]\n");
+    fprintf(stderr, "    -p, --peak-symmetry <float>    peak symmetry threshold (0-1, larger is stricter) [0.5]\n");
     fprintf(stderr, "\n");
     exit(1);
 }
@@ -608,12 +646,23 @@ int main_polysomy(int argc, char *argv[])
     args_t *args = (args_t*) calloc(1,sizeof(args_t));
     args->argc   = argc; args->argv = argv;
     args->nbins  = 150;
-    args->fit_th = 3.0;
+    args->fit_th = 3.3;
     args->cn_penalty = 0.7;
-    args->peak_symmetry = 0.7;
+    args->peak_symmetry = 0.5;
+    args->min_peak_size = 0.1;
+    args->ra_rr_scaling = 1;
+    args->min_fraction = 0.1;
+    args->smooth = -3;
 
-    static struct option loptions[] = 
+    static struct option loptions[] =
     {
+        {"ra-rr-scaling",0,0,1},    // hidden option
+        {"force-cn",1,0,2},         // hidden option
+        {"smooth",1,0,'S'},         // hidden option
+        {"nbins",1,0,'n'},          // hidden option
+        {"include-aa",0,0,'i'},
+        {"peak-size",1,0,'b'},
+        {"min-fraction",1,0,'m'},
         {"verbose",0,0,'v'},
         {"fit-th",1,0,'f'},
         {"cn-penalty",1,0,'c'},
@@ -627,19 +676,34 @@ int main_polysomy(int argc, char *argv[])
         {0,0,0,0}
     };
     char c, *tmp;
-    while ((c = getopt_long(argc, argv, "h?o:vt:T:r:R:s:f:p:c:",loptions,NULL)) >= 0) 
+    while ((c = getopt_long(argc, argv, "h?o:vt:T:r:R:s:f:p:c:im:b:n:S:",loptions,NULL)) >= 0)
     {
-        switch (c) 
+        switch (c)
         {
-            case 'f': 
+            case  1 : args->ra_rr_scaling = 0; break;
+            case  2 : args->force_cn = atoi(optarg); break;
+            case 'n': args->nbins = atoi(optarg); break;
+            case 'S': args->smooth = atoi(optarg); break;
+            case 'i': args->include_aa = 1; break;
+            case 'b':
+                args->min_peak_size = strtod(optarg,&tmp);
+                if ( *tmp ) error("Could not parse: -b %s\n", optarg);
+                if ( args->min_peak_size<0 || args->min_peak_size>1 ) error("Range error: -b %s\n", optarg);
+                break;
+            case 'm':
+                args->min_fraction = strtod(optarg,&tmp);
+                if ( *tmp ) error("Could not parse: -n %s\n", optarg);
+                if ( args->min_fraction<0 || args->min_fraction>1 ) error("Range error: -n %s\n", optarg);
+                break;
+            case 'f':
                 args->fit_th = strtod(optarg,&tmp);
                 if ( *tmp ) error("Could not parse: -f %s\n", optarg);
                 break;
-            case 'p': 
+            case 'p':
                 args->peak_symmetry = strtod(optarg,&tmp);
                 if ( *tmp ) error("Could not parse: -p %s\n", optarg);
                 break;
-            case 'c': 
+            case 'c':
                 args->cn_penalty = strtod(optarg,&tmp);
                 if ( *tmp ) error("Could not parse: -c %s\n", optarg);
                 break;
@@ -649,7 +713,7 @@ int main_polysomy(int argc, char *argv[])
             case 'r': args->regions_list = optarg; break;
             case 'R': args->regions_list = optarg; args->regions_is_file = 1; break;
             case 'o': args->output_dir = optarg; break;
-            case 'v': args->verbose = 1; break;
+            case 'v': args->verbose++; break;
             default: usage(args); break;
         }
     }
diff --git a/rbuf.h b/rbuf.h
index 89ff9aa..3d2805c 100644
--- a/rbuf.h
+++ b/rbuf.h
@@ -174,23 +174,28 @@ static inline void rbuf_shift_n(rbuf_t *rbuf, int n)
  *  rbuf_expand0() - expand round buffer and set the newly allocated elements to 0
  *  @rbuf:      the rbuf holder
  *  @type_t:    data type
+ *  @n:         requested number of elements
  *  @data:      data array to be realloced
  *
  *  Note: The new array is linearized and leaves the rbuf.f offset untouched,
  *  thus the size of the new buffer is determined by the current position.
  */
-#define rbuf_expand0(rbuf,type_t,data) { \
-    int m = (rbuf)->m + (rbuf)->f + 1; \
-    m--, m|=m>>1, m|=m>>2, m|=m>>4, m|=m>>8, m|=m>>16, m++; /* kroundup32 */ \
-    data = (type_t*) realloc(data, sizeof(type_t)*m); \
-    type_t *ptr = data; \
-    memset(ptr+(rbuf)->m,0,sizeof(type_t)*(m-(rbuf)->m)); \
-    if ( (rbuf)->f ) \
+#define rbuf_expand0(rbuf,type_t,n,data) \
+{ \
+    if ( n > (rbuf)->m ) \
     { \
-        memcpy(ptr+(rbuf)->m,ptr,sizeof(type_t)*(rbuf)->f); \
-        memset(ptr,0,sizeof(type_t)*(rbuf)->f); \
+        int m = n + (rbuf)->f; \
+        m--, m|=m>>1, m|=m>>2, m|=m>>4, m|=m>>8, m|=m>>16, m++; /* kroundup32 */ \
+        data = (type_t*) realloc(data, sizeof(type_t)*m); \
+        type_t *ptr = data; \
+        memset(ptr+(rbuf)->m,0,sizeof(type_t)*(m-(rbuf)->m)); \
+        if ( (rbuf)->f ) \
+        { \
+            memcpy(ptr+(rbuf)->m,ptr,sizeof(type_t)*(rbuf)->f); \
+            memset(ptr,0,sizeof(type_t)*(rbuf)->f); \
+        } \
+        (rbuf)->m = m; \
     } \
-    (rbuf)->m = m; \
 }
 
 #endif
diff --git a/test/annotate4.out b/test/annotate4.out
index 6740242..934cf89 100644
--- a/test/annotate4.out
+++ b/test/annotate4.out
@@ -13,7 +13,7 @@
 ##FILTER=<ID=q11,Description="Quality below 10">
 ##FILTER=<ID=q99,Description="Quality below 10">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	A	B	C
-1	3000001	xx	C	T	11	.	IINT=11;IFLT=1.1;ISTR=xxx	GT:FINT:FFLT:FSTR	.:11:1.1:xxx	.:11:1.1:x	0/0:11:1.1:x
+1	3000001	xx	C	T	11	PASS	IINT=11;IFLT=1.1;ISTR=xxx	GT:FINT:FFLT:FSTR	.:11:1.1:xxx	.:11:1.1:x	0/0:11:1.1:x
 1	3000002	id	C	T	99	q99	FLAG;IINT=88,99;IFLT=8.8,9.9;ISTR=888,999	GT:FINT:FFLT:FSTR	0|1:77:7.7:77	1|1:88,99:8.8,9.9:888,999	.:.:.:.
 1	3000003	id	C	T	99	q99	FLAG;IINT=88,99;IFLT=8.8,9.9;ISTR=888,999	GT:FINT:FFLT:FSTR	0|1:77:7.7:77	1|1:88,99:8.8,9.9:888,999	0/0:.:.:.
 1	3000004	id	C	T	99	q99	FLAG;IINT=88,99;IFLT=8.8,9.9;ISTR=888,999	GT:FINT:FFLT:FSTR	0|1:77:7.7:77	1|1:88,99:8.8,9.9:888,999	0/0:11:1.1:xxx
diff --git a/test/annotate5.out b/test/annotate5.out
index d3ab764..a57261e 100644
--- a/test/annotate5.out
+++ b/test/annotate5.out
@@ -15,5 +15,5 @@
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	A	B	C
 1	3000001	xx	C	T	11	PASS	IINT=11;IFLT=1.1;ISTR=xxx	GT:FINT:FFLT:FSTR	.:11:1.1:xxx	0/0:11:1.1:x	0/0:11:1.1:x
 1	3000002	id	C	T	99	q99	FLAG;IINT=88,99;IFLT=8.8,9.9;ISTR=888,999	GT	0|1	.	.
-1	3000003	id	C	T	99	q11;q99	FLAG;IINT=88,99;IFLT=8.8,9.9;ISTR=888,999	GT:FINT:FFLT:FSTR	0|1:.:.:.	0/0:.:.:.	0/0:.:.:.
-1	3000004	id	C	T	99	q11;q99	FLAG;IINT=11;IFLT=1.1;ISTR=xxx	GT:FINT:FFLT:FSTR	0|1:11:1.1:x	0/0:11:1.1:xxx	0/0:11:1.1:xxx
+1	3000003	id	C	T	99	q11	FLAG;IINT=88,99;IFLT=8.8,9.9;ISTR=888,999	GT:FINT:FFLT:FSTR	0|1:.:.:.	0/0:.:.:.	0/0:.:.:.
+1	3000004	id	C	T	99	q11	FLAG;IINT=11;IFLT=1.1;ISTR=xxx	GT:FINT:FFLT:FSTR	0|1:11:1.1:x	0/0:11:1.1:xxx	0/0:11:1.1:xxx
diff --git a/test/merge.2.b.vcf b/test/annotate9.out
similarity index 72%
copy from test/merge.2.b.vcf
copy to test/annotate9.out
index fab439f..66c872d 100644
--- a/test/merge.2.b.vcf
+++ b/test/annotate9.out
@@ -1,4 +1,5 @@
 ##fileformat=VCFv4.1
+##FILTER=<ID=PASS,Description="All filters passed">
 ##INFO=<ID=TEST,Number=1,Type=Integer,Description="Testing Tag">
 ##FORMAT=<ID=TT,Number=A,Type=Integer,Description="Testing Tag, with commas and \"escapes\" and escaped escapes combined with \\\"quotes\\\\\"">
 ##INFO=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
@@ -12,6 +13,7 @@
 ##contig=<ID=2,assembly=b37,length=249250621>
 ##contig=<ID=3,assembly=b37,length=198022430>
 ##contig=<ID=4,assembly=b37,length=191154276>
+##test=<ID=4,IE=5>
 ##reference=file:///lustre/scratch105/projects/g1k/ref/main_project/human_g1k_v37.fasta
 ##readme=AAAAAA
 ##readme=BBBBBB
@@ -20,11 +22,8 @@
 ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
 ##INFO=<ID=STR,Number=1,Type=String,Description="Test string type">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	A	B
-1	3000000	.	C	G	59.2	PASS	AN=4;AC=2	GT:GQ	0/1:245	0/1:245
-1	3000150	.	C	G	59.2	PASS	AN=4;AC=2	GT:GQ	0/1:245	0/1:245
-1	3000151	.	C	G	59.2	PASS	AN=4;AC=2	GT:DP:GQ	0/1:32:245	0/1:32:245
-1	3106154	.	C	CCC	342	PASS	AN=4;AC=2	GT:GQ:DP	0/1:245:32	0/1:245:32
-1	3106154	.	C	T	59.2	PASS	AN=4;AC=2	GT:GQ:DP	0/1:245:32	0/1:245:32
-1	3200000	.	C	T	59.2	PASS	AN=4;AC=2	GT:GQ:DP	0/1:245:32	0/1:245:32
-1	3200010	.	C	A,T	59.2	PASS	AN=4;AC=2	GT:GQ:DP	0/1:245:32	0/1:245:32
-1	3200020	.	C	T,G	59.2	PASS	AN=4;AC=2	GT:GL	./.:1,4,6,2,5,3	.:1,3,2
+1	3000150	id150	C	T	59.2	PASS	AN=4;AC=2	GT:GQ	0/1:245	0/1:245
+1	3000151	id3000151	C	T	59.2	PASS	AN=4;AC=2	GT:DP:GQ	0/1:32:245	0/1:32:245
+1	3062915	id3D	GTTT	G	12.9	q10	DP4=1,2,3,4;AN=4;AC=2;INDEL;STR=test	GT:GQ:DP:GL	0/1:409:35:-20,-5,-20	0/1:409:35:-20,-5,-20
+1	3062915	idSNP	G	T,C	12.6	test	TEST=5;DP4=1,2,3,4;AN=3;AC=1,1	GT:TT:GQ:DP:GL	0/1:0,1:409:35:-20,-5,-20,-20,-5,-20	2:0,1:409:35:-20,-5,-20
+1	3106154	id3106154	CAAA	C	342	PASS	AN=4;AC=2	GT:GQ:DP	0/1:245:32	0/1:245:32
diff --git a/test/merge.2.b.vcf b/test/annotate9.vcf
similarity index 73%
copy from test/merge.2.b.vcf
copy to test/annotate9.vcf
index fab439f..6595167 100644
--- a/test/merge.2.b.vcf
+++ b/test/annotate9.vcf
@@ -12,6 +12,7 @@
 ##contig=<ID=2,assembly=b37,length=249250621>
 ##contig=<ID=3,assembly=b37,length=198022430>
 ##contig=<ID=4,assembly=b37,length=191154276>
+##test=<ID=4,IE=5>
 ##reference=file:///lustre/scratch105/projects/g1k/ref/main_project/human_g1k_v37.fasta
 ##readme=AAAAAA
 ##readme=BBBBBB
@@ -20,11 +21,8 @@
 ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
 ##INFO=<ID=STR,Number=1,Type=String,Description="Test string type">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	A	B
-1	3000000	.	C	G	59.2	PASS	AN=4;AC=2	GT:GQ	0/1:245	0/1:245
-1	3000150	.	C	G	59.2	PASS	AN=4;AC=2	GT:GQ	0/1:245	0/1:245
-1	3000151	.	C	G	59.2	PASS	AN=4;AC=2	GT:DP:GQ	0/1:32:245	0/1:32:245
-1	3106154	.	C	CCC	342	PASS	AN=4;AC=2	GT:GQ:DP	0/1:245:32	0/1:245:32
-1	3106154	.	C	T	59.2	PASS	AN=4;AC=2	GT:GQ:DP	0/1:245:32	0/1:245:32
-1	3200000	.	C	T	59.2	PASS	AN=4;AC=2	GT:GQ:DP	0/1:245:32	0/1:245:32
-1	3200010	.	C	A,T	59.2	PASS	AN=4;AC=2	GT:GQ:DP	0/1:245:32	0/1:245:32
-1	3200020	.	C	T,G	59.2	PASS	AN=4;AC=2	GT:GL	./.:1,4,6,2,5,3	.:1,3,2
+1	3000150	id150	C	T	59.2	PASS	AN=4;AC=2	GT:GQ	0/1:245	0/1:245
+1	3000151	.	C	T	59.2	PASS	AN=4;AC=2	GT:DP:GQ	0/1:32:245	0/1:32:245
+1	3062915	id3D	GTTT	G	12.9	q10	DP4=1,2,3,4;AN=4;AC=2;INDEL;STR=test	GT:GQ:DP:GL	0/1:409:35:-20,-5,-20	0/1:409:35:-20,-5,-20
+1	3062915	idSNP	G	T,C	12.6	test	TEST=5;DP4=1,2,3,4;AN=3;AC=1,1	GT:TT:GQ:DP:GL	0/1:0,1:409:35:-20,-5,-20,-20,-5,-20	2:0,1:409:35:-20,-5,-20
+1	3106154	.	CAAA	C	342	PASS	AN=4;AC=2	GT:GQ:DP	0/1:245:32	0/1:245:32
diff --git a/test/annots9.tab b/test/annots9.tab
new file mode 100644
index 0000000..678e3c4
--- /dev/null
+++ b/test/annots9.tab
@@ -0,0 +1,5 @@
+1	3000150	C	T	id3000150
+1	3000151	C	T	id3000151
+1	3062915	GTTT	G	id3062915_3D
+1	3062915	G	T,C	id3062915_NP
+1	3106154	CAAA	C	id3106154
diff --git a/test/merge.2.b.vcf b/test/annots9.vcf
similarity index 73%
copy from test/merge.2.b.vcf
copy to test/annots9.vcf
index fab439f..6ff2cce 100644
--- a/test/merge.2.b.vcf
+++ b/test/annots9.vcf
@@ -12,6 +12,7 @@
 ##contig=<ID=2,assembly=b37,length=249250621>
 ##contig=<ID=3,assembly=b37,length=198022430>
 ##contig=<ID=4,assembly=b37,length=191154276>
+##test=<ID=4,IE=5>
 ##reference=file:///lustre/scratch105/projects/g1k/ref/main_project/human_g1k_v37.fasta
 ##readme=AAAAAA
 ##readme=BBBBBB
@@ -20,11 +21,8 @@
 ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
 ##INFO=<ID=STR,Number=1,Type=String,Description="Test string type">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	A	B
-1	3000000	.	C	G	59.2	PASS	AN=4;AC=2	GT:GQ	0/1:245	0/1:245
-1	3000150	.	C	G	59.2	PASS	AN=4;AC=2	GT:GQ	0/1:245	0/1:245
-1	3000151	.	C	G	59.2	PASS	AN=4;AC=2	GT:DP:GQ	0/1:32:245	0/1:32:245
-1	3106154	.	C	CCC	342	PASS	AN=4;AC=2	GT:GQ:DP	0/1:245:32	0/1:245:32
-1	3106154	.	C	T	59.2	PASS	AN=4;AC=2	GT:GQ:DP	0/1:245:32	0/1:245:32
-1	3200000	.	C	T	59.2	PASS	AN=4;AC=2	GT:GQ:DP	0/1:245:32	0/1:245:32
-1	3200010	.	C	A,T	59.2	PASS	AN=4;AC=2	GT:GQ:DP	0/1:245:32	0/1:245:32
-1	3200020	.	C	T,G	59.2	PASS	AN=4;AC=2	GT:GL	./.:1,4,6,2,5,3	.:1,3,2
+1	3000150	id3000150	C	T	59.2	PASS	AN=4;AC=2	GT:GQ	0/1:245	0/1:245
+1	3000151	id3000151	C	T	59.2	PASS	AN=4;AC=2	GT:DP:GQ	0/1:32:245	0/1:32:245
+1	3062915	id3062915_3D	GTTT	G	12.9	q10	DP4=1,2,3,4;AN=4;AC=2;INDEL;STR=test	GT:GQ:DP:GL	0/1:409:35:-20,-5,-20	0/1:409:35:-20,-5,-20
+1	3062915	id3062915_NP	G	T,C	12.6	test	TEST=5;DP4=1,2,3,4;AN=3;AC=1,1	GT:TT:GQ:DP:GL	0/1:0,1:409:35:-20,-5,-20,-20,-5,-20	2:0,1:409:35:-20,-5,-20
+1	3106154	id3106154	CAAA	C	342	PASS	AN=4;AC=2	GT:GQ:DP	0/1:245:32	0/1:245:32
diff --git a/test/check.chk b/test/check.chk
index 1012e5c..7792e00 100644
--- a/test/check.chk
+++ b/test/check.chk
@@ -5,6 +5,7 @@
 # SN	[2]id	[3]key	[4]value
 SN	0	number of samples:	2
 SN	0	number of records:	18
+SN	0	number of no-ALTs:	1
 SN	0	number of SNPs:	5
 SN	0	number of MNPs:	1
 SN	0	number of indels:	9
@@ -68,10 +69,16 @@ DP	0	30	2	5.555556	0	0.000000
 DP	0	31	16	44.444444	0	0.000000
 DP	0	32	4	11.111111	0	0.000000
 DP	0	35	4	11.111111	0	0.000000
+DP	0	60	0	0.000000	1	33.333333
+DP	0	62	0	0.000000	2	66.666667
 # PSC, Per-sample counts
 # PSC	[2]id	[3]sample	[4]nRefHom	[5]nNonRefHom	[6]nHets	[7]nTransitions	[8]nTransversions	[9]nIndels	[10]average depth	[11]nSingletons
-PSC	0	A	0	2	3	3	2	9	28.7	1
-PSC	0	B	1	1	3	2	2	9	28.7	0
+PSC	0	A	0	2	4	3	2	9	28.7	1
+PSC	0	B	1	1	4	2	2	9	28.7	0
+# PSI, Per-Sample Indels
+# PSI	[2]id	[3]sample	[4]in-frame	[5]out-frame	[6]not applicable	[7]out/(in+out) ratio	[8]nHets	[9]nAA
+PSI	0	A	0	0	0	0.00	9	0
+PSI	0	B	0	0	0	0.00	9	0
 # HWE
 # HWE	[2]id	[3]1st ALT allele frequency	[4]Number of observations	[5]25th percentile	[6]median	[7]75th percentile
 HWE	0	0.000000	2	0.490000	0.490000	0.990000
diff --git a/test/check.vcf b/test/check.vcf
index 8fe38e4..055fd43 100644
--- a/test/check.vcf
+++ b/test/check.vcf
@@ -1,6 +1,7 @@
 ##fileformat=VCFv4.1
 ##INFO=<ID=TEST,Number=1,Type=Integer,Description="Testing Tag">
 ##FORMAT=<ID=TT,Number=A,Type=Integer,Description="Testing Tag, with commas and \"escapes\" and escaped escapes combined with \\\"quotes\\\\\"">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="read depth">
 ##INFO=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
@@ -27,9 +28,9 @@
 1	3184885	.	TAAAA	TA,T	61.5	PASS	AN=4;AC=2,2	GT:GQ:DP	1/2:12:10	1/2:12:10
 2	3199812	.	G	GTT,GT	82.7	PASS	AN=4;AC=2,2	GT:GQ:DP	1/2:322:26	1/2:322:26
 3	3212016	.	CTT	C,CT	79	PASS	AN=4;AC=2,2	GT:GQ:DP	1/2:91:26	1/2:91:26
-4	3258448	.	TACACACAC	T	59.9	PASS	AN=4;AC=2	GT:GQ:DP	0/1:325:31	0/1:325:31
-4	3258449	.	GCAAA	GA,G	59.9	PASS	AN=4;AC=2	GT:GQ:DP	0/1:325:31	0/1:325:31
-4	3258450	.	AAAAGAAAAAG	A,AAAAAAG	59.9	PASS	AN=4;AC=2	GT:GQ:DP	0/1:325:31	0/1:325:31
+4	3258448	.	TACACACAC	T	59.9	PASS	DP=62;AN=4;AC=2	GT:GQ:DP	0/1:325:31	0/1:325:31
+4	3258449	.	GCAAA	GA,G	59.9	PASS	DP=62;AN=4;AC=2	GT:GQ:DP	0/1:325:31	0/1:325:31
+4	3258450	.	AAAAGAAAAAG	A,AAAAAAG	59.9	PASS	DP=60;AN=4;AC=2	GT:GQ:DP	0/1:325:31	0/1:325:31
 4	3258451	.	AAA	AGT	59.9	PASS	AN=4;AC=2	GT:GQ:DP	0/1:325:31	0/1:325:31
 4	3258452	.	AAA	AGA	59.9	PASS	AN=4;AC=2	GT:GQ:DP	0/1:325:31	0/1:325:31
 4	3258453	.	AACA	AGA	59.9	PASS	AN=4;AC=2	GT:GQ:DP	0/1:325:31	0/1:325:31
diff --git a/test/check.chk b/test/check_merge.chk
similarity index 62%
copy from test/check.chk
copy to test/check_merge.chk
index 1012e5c..3df3bae 100644
--- a/test/check.chk
+++ b/test/check_merge.chk
@@ -1,40 +1,30 @@
 #
-# Definition of sets:
+# Definition of sets
 # ID	[2]id	[3]tab-separated file names
-# SN, Summary numbers:
+# SN, Summary numbers
 # SN	[2]id	[3]key	[4]value
 SN	0	number of samples:	2
 SN	0	number of records:	18
+SN	0	number of no-ALTs:	1
 SN	0	number of SNPs:	5
 SN	0	number of MNPs:	1
 SN	0	number of indels:	9
 SN	0	number of others:	2
 SN	0	number of multiallelic sites:	6
 SN	0	number of multiallelic SNP sites:	1
-# TSTV, transitions/transversions:
+# # TSTV, transition/transversions:
 # TSTV	[2]id	[3]ts	[4]tv	[5]ts/tv	[6]ts (1st ALT)	[7]tv (1st ALT)	[8]ts/tv (1st ALT)
 TSTV	0	3	2	1.50	3	1	3.00
-# SiS, Singleton stats:
+# Sis, Singleton stats
 # SiS	[2]id	[3]allele count	[4]number of SNPs	[5]number of transitions	[6]number of transversions	[7]number of indels	[8]repeat-consistent	[9]repeat-inconsistent	[10]not applicable
 SiS	0	1	3	1	2	0	0	0	0
-# AF, Stats by non-reference allele frequency:
+# AF, Stats by non-reference allele frequency
 # AF	[2]id	[3]allele frequency	[4]number of SNPs	[5]number of transitions	[6]number of transversions	[7]number of indels	[8]repeat-consistent	[9]repeat-inconsistent	[10]not applicable
 AF	0	0.000000	3	1	2	2	0	0	2
 AF	0	49.000000	0	0	0	12	0	0	12
 AF	0	74.000000	1	1	0	0	0	0	0
 AF	0	99.000000	1	1	0	0	0	0	0
-# QUAL, Stats by quality:
-# QUAL	[2]id	[3]Quality	[4]number of SNPs	[5]number of transitions (1st ALT)	[6]number of transversions (1st ALT)	[7]number of indels
-QUAL	0	12	1	0	1	1
-QUAL	0	45	0	0	0	1
-QUAL	0	59	2	1	0	3
-QUAL	0	60	1	1	0	0
-QUAL	0	61	0	0	0	1
-QUAL	0	79	0	0	0	1
-QUAL	0	82	0	0	0	1
-QUAL	0	90	1	1	0	0
-QUAL	0	342	0	0	0	1
-# IDD, InDel distribution:
+# IDD, InDel distribution
 # IDD	[2]id	[3]length (deletions negative)	[4]count
 IDD	0	-10	1
 IDD	0	-8	1
@@ -44,7 +34,7 @@ IDD	0	-2	1
 IDD	0	-1	2
 IDD	0	1	1
 IDD	0	2	1
-# ST, Substitution types:
+# ST, Substitution types
 # ST	[2]id	[3]type	[4]count
 ST	0	A>C	0
 ST	0	A>G	0
@@ -60,21 +50,16 @@ ST	0	T>C	0
 ST	0	T>G	0
 # DP, Depth distribution
 # DP	[2]id	[3]bin	[4]number of genotypes	[5]fraction of genotypes (%)	[6]number of sites	[7]fraction of sites (%)
-DP	0	10	2	5.555556	0	0.000000
-DP	0	21	2	5.555556	0	0.000000
-DP	0	22	2	5.555556	0	0.000000
-DP	0	26	4	11.111111	0	0.000000
-DP	0	30	2	5.555556	0	0.000000
-DP	0	31	16	44.444444	0	0.000000
-DP	0	32	4	11.111111	0	0.000000
-DP	0	35	4	11.111111	0	0.000000
-# PSC, Per-sample counts
-# PSC	[2]id	[3]sample	[4]nRefHom	[5]nNonRefHom	[6]nHets	[7]nTransitions	[8]nTransversions	[9]nIndels	[10]average depth	[11]nSingletons
-PSC	0	A	0	2	3	3	2	9	28.7	1
-PSC	0	B	1	1	3	2	2	9	28.7	0
-# HWE
-# HWE	[2]id	[3]1st ALT allele frequency	[4]Number of observations	[5]25th percentile	[6]median	[7]75th percentile
-HWE	0	0.000000	2	0.490000	0.490000	0.990000
-HWE	0	49.000000	14	0.990000	0.990000	0.990000
-HWE	0	74.000000	1	0.490000	0.490000	0.490000
-HWE	0	99.000000	1	0.000000	0.000000	0.000000
+DP	0	60	0	0.000000	1	33.333333
+DP	0	62	0	0.000000	2	66.666667
+# QUAL, Stats by quality
+# QUAL	[2]id	[3]Quality	[4]number of SNPs	[5]number of transitions (1st ALT)	[6]number of transversions (1st ALT)	[7]number of indels
+QUAL	0	12	1	0	1	1
+QUAL	0	45	0	0	0	1
+QUAL	0	59	2	1	0	3
+QUAL	0	60	1	1	0	0
+QUAL	0	61	0	0	0	1
+QUAL	0	79	0	0	0	1
+QUAL	0	82	0	0	0	1
+QUAL	0	90	1	1	0	0
+QUAL	0	342	0	0	0	1
diff --git a/test/consensus.5.out b/test/consensus.5.out
new file mode 100644
index 0000000..4631ebe
--- /dev/null
+++ b/test/consensus.5.out
@@ -0,0 +1,20 @@
+>1:2-501
+TACCATATGTGACATATAAAAAAGAACATAACCTACGTATCAACTAAAGTGGTTGTTTGC
+AGAAAAGGAAGACTTAAAAAGAGTCAGTACTAACCTACATAATATATACAATGTTCATTA
+AATAATAAAATGAGCTCATCATACTTAGGTCATCATAAATATATCTGAAATTCACAAATA
+TTGATCAAATGGTAAAATAGACAAGTAGATTTTAATAGGTTAAACAATTACTGATTCTCT
+TGAAAGAATAAATTTAATATGAGACCTATTTCATTATAATGAACTCACAAATTAGAAACT
+TCACACTGGGGGCTGGAGAGATGGCTCAGTAGTTAAGAACACTGACTGCTCTTCTGAAGG
+TCCTGAGTTCAAATCCCAGCAACCACATGGTGACTTACAACCATCTGTAATGACATCTGA
+TGCCCTCTGGTGTGTCTGAAGACAGCTACAGTGTACTTACATAAAATAATAAATAAATCT
+TTAAAAACAAAAAAAAAGAA
+>2
+GAAGATCTTTTCCTTATTAAGGATCTGAAGCTCTGTAGATTTGTATTCTATTAAACATGG
+AGAGATTAGTGATTTTCCATATTCTTTAAGTCATTTTAGAGTAATGTGTTCTTAAGATAA
+ATCAGAAAAACAAAAACTTGTGCTTTCCTGTTTGAAAAACAAACAGCTGTGGGGAATGGT
+GTCGGGACAGCCTTTTTATAAAATTTTTCTAAATAATGTTGAGGCTTTGATACGTCAAAG
+TTATATTTCAAATGGAATCACTTAGACCTCGTTTCTGAGTGTCAATGGCCATATTGGGGA
+TTTGCTGCTGCCAATGACAGCACACCCTGGGAATGCCCCAACTACTTACTACAAAGCAGT
+GTTACATGGAGAAGATCTTCAAGAGTCTTTTTGCTAGATCTTTCCTTGGCTTTTGATGTG
+ACTCCTCTCAATAAAATCCACAGTAATATAGTGAGTGGTCTCCTGCTCCAAACCAGTATT
+TCAGACACAGTTAATCCAGAC
diff --git a/test/consensus2.1.out b/test/consensus2.1.out
new file mode 100644
index 0000000..65ec852
--- /dev/null
+++ b/test/consensus2.1.out
@@ -0,0 +1,10 @@
+>1
+CTACCATATGTGACATATAAAAAAGAACATAACCTACGTATCAACTAAAGTGGTTGTTA
+>2
+CCTACCATATGTGACATATAAAAAAGAACATAACCTACGTATCAACTAAAGTGGTTGTTA
+>3
+CCCTACCATATGTGACATATAAAAAAGAACATAACCTACGTATCAACTAAAGTGGTTGTT
+A
+>4
+CCCCTACCATATGTGACATATAAAAAAGAACATAACCTACGTATCAACTAAAGTGGTTGT
+TA
diff --git a/test/consensus2.2.out b/test/consensus2.2.out
new file mode 100644
index 0000000..2040354
--- /dev/null
+++ b/test/consensus2.2.out
@@ -0,0 +1,12 @@
+>1
+CTACCATATGTGACATATAAAAAAGAACATAACCTACGTATCAACTAAAGTGGTTGTTCA
+A
+>2
+CCTACCATATGTGACATATAAAAAAGAACATAACCTACGTATCAACTAAAGTGGTTGTTC
+AA
+>3
+CCCTACCATATGTGACATATAAAAAAGAACATAACCTACGTATCAACTAAAGTGGTTGTT
+CAA
+>4
+CCCCTACCATATGTGACATATAAAAAAGAACATAACCTACGTATCAACTAAAGTGGTTGT
+TCAA
diff --git a/test/consensus2.fa b/test/consensus2.fa
new file mode 100644
index 0000000..9f3522f
--- /dev/null
+++ b/test/consensus2.fa
@@ -0,0 +1,10 @@
+>1
+CTACCATATGTGACATATAAAAAAGAACATAACCTACGTATCAACTAAAGTGGTTGTTC
+>2
+CCTACCATATGTGACATATAAAAAAGAACATAACCTACGTATCAACTAAAGTGGTTGTTC
+>3
+CCCTACCATATGTGACATATAAAAAAGAACATAACCTACGTATCAACTAAAGTGGTTGTT
+C
+>4
+CCCCTACCATATGTGACATATAAAAAAGAACATAACCTACGTATCAACTAAAGTGGTTGT
+TC
diff --git a/test/consensus2.vcf b/test/consensus2.vcf
new file mode 100644
index 0000000..ca4c059
--- /dev/null
+++ b/test/consensus2.vcf
@@ -0,0 +1,9 @@
+##fileformat=VCFv4.2
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
+##ALT=<ID=DEL,Description="Deletion">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA001
+1	59	.	C	a,Caa	.	PASS	.	GT	1|2
+2	60	.	C	a,Caa	.	PASS	.	GT	1|2
+3	61	.	C	a,Caa	.	PASS	.	GT	1|2
+4	62	.	C	a,Caa	.	PASS	.	GT	1|2
diff --git a/test/convert.gs.gt.gen b/test/convert.gs.gt.gen
index 01e8a73..e209a57 100644
--- a/test/convert.gs.gt.gen
+++ b/test/convert.gs.gt.gen
@@ -9,7 +9,7 @@ X:2698889_T_C X:2698889_T_C 2698889 T C 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0
 X:2698923_G_A X:2698923_G_A 2698923 G A 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0
 X:2698953_A_AGG X:2698953_A_AGG 2698953 A AGG 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0
 X:2698954_G_A X:2698954_G_A 2698954 G A 0 1 0 0 0 1 0 1 0 0 1 0 0 1 0 1 0 0 1 0 0 0 1 0 1 0 0 1 0 0
-X:2699002_C_A X:2699002_C_A 2699002 C A 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0
+X:2699002_C_A X:2699002_C_A 2699002 C A 1 0 0 1 0 0 0.33 0.33 0.33 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0
 X:2699025_T_C X:2699025_T_C 2699025 T C 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0
 X:2699091_G_A X:2699091_G_A 2699091 G A 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0
 X:2699187_T_C X:2699187_T_C 2699187 T C 1 0 0 1 0 0 0 1 0 1 0 0 0 1 0 0 1 0 0 1 0 1 0 0 1 0 0 0 1 0
diff --git a/test/convert.gt.noHead.vcf b/test/convert.gt.noHead.vcf
new file mode 100644
index 0000000..53cdd85
--- /dev/null
+++ b/test/convert.gt.noHead.vcf
@@ -0,0 +1,36 @@
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA00001	NA00002	NA00003	NA00004	NA00005	NA00006	NA00007	NA00008	NA00009	NA00010
+X	2698560	.	G	A	.	.	.	GT	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0
+X	2698630	.	A	G	.	.	.	GT	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0
+X	2698758	.	CAA	C	.	.	.	GT	0|0	0|1	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0
+X	2698769	.	AAG	A	.	.	.	GT	1|0	1|1	0|1	1|0	1|0	0|0	0|0	0|0	0|0	0|0
+X	2698770	.	AG	A	.	.	.	GT	0|0	0|1	0|0	0|0	1|0	0|0	0|0	0|0	0|0	0|0
+X	2698770	.	AG	AAGG	.	.	.	GT	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0
+X	2698789	.	C	G	.	.	.	GT	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0
+X	2698822	.	A	C	.	.	.	GT	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0
+X	2698831	.	G	A	.	.	.	GT	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0
+X	2698889	.	T	C	.	.	.	GT	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0
+X	2698923	.	G	A	.	.	.	GT	1|0	0|1	0|1	1|0	1|0	0|0	0|0	0|0	0|0	0|0
+X	2698953	.	A	AGG	.	.	.	GT	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0
+X	2698954	.	G	A	.	.	.	GT	1|0	1|1	0|1	1|0	1|0	0|0	0|0	0|1	0|0	0|0
+X	2699002	.	C	A	.	.	.	GT	0|0	0|0	.|.	0|0	0|0	0|0	0|0	0|0	0|0	0|0
+X	2699025	.	T	C	.	.	.	GT	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0
+X	2699091	.	G	A	.	.	.	GT	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0
+X	2699187	.	T	C	.	.	.	GT	0|0	0|0	1|0	0|0	0|1	1|0	1|0	0|0	0|0	0/1
+X	2699188	.	G	C	.	.	.	GT	0|0	0|0	1|0	0|0	0|1	1|0	1|0	0|0	0|0	0|1
+X	2699189	.	T	C	.	.	.	GT	0|0	0|0	1|0	0|0	0|1	1|0	1|0	0|0	0|0	0|1
+X	2699217	.	C	T	.	.	.	GT	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0
+X	2699246	.	C	A	.	.	.	GT	1|0	1|1	0|1	1|1	1|0	0|1	0|0	0|1	0|0	1|0
+X	2699275	.	T	G	.	.	.	GT	0|0	0|0	1|0	0|0	0|1	1|1	1|0	0|0	0|0	0|1
+X	2699350	.	A	T	.	.	.	GT	0|0	0|0	1|0	0|0	0|1	1|0	1|0	0|0	0|0	0|1
+X	2699360	.	T	C	.	.	.	GT	0|0	0|0	1|0	0|0	0|1	1|0	1|0	0|0	0|0	0|1
+X	2699450	.	A	C	.	.	.	GT	0|0	0|0	1|0	0|0	0|1	1|0	1|0	0|0	0|0	0|1
+X	2699507	.	T	C	.	.	.	GT	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0
+X	2699555	.	C	A	.	.	.	GT	0	1	1	0	1	1|1	1|0	0|1	0|0	0|1
+X	2699645	.	G	T	.	.	.	GT	0	1	0	0	0	0|0	0|0	0|1	0|0	0|0
+X	2699676	.	G	A	.	.	.	GT	0	0	1	0	1	1|0	1|0	0|0	0|0	0|1
+X	2699728	.	C	T	.	.	.	GT	0	0	0	0	0	0|0	0|0	0|0	0|0	0|0
+X	2699775	.	C	A	.	.	.	GT	0	0	0	0	0	0|0	0|0	0|0	0|0	0|0
+X	2699898	.	C	CT	.	.	.	GT	0	0	1	0	1	1|0	1|0	0|0	0|0	0|1
+X	2699968	.	A	G	.	.	.	GT	.	0	0	1	0	0|1	0|0	0|0	0|1	1|0
+X	2699970	.	T	C	.	.	.	GT	0	0	0	0	0	0|0	0|0	0|0	0|0	0|0
+X	2699990	.	C	<INS:ME:LINE1>	.	.	END=2700054	GT	0|0	0|0	1|0	0|0	0|1	1|0	1|0	0|0	0|0	0|1
diff --git a/test/convert.gt.vcf b/test/convert.gt.vcf
new file mode 100644
index 0000000..7c719a2
--- /dev/null
+++ b/test/convert.gt.vcf
@@ -0,0 +1,43 @@
+##fileformat=VCFv4.1
+##FILTER=<ID=PASS,Description="All filters passed">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##contig=<ID=X,assembly=b37,length=155270560>
+##bcftools_normVersion=1.2+htslib-1.2.1
+##bcftools_normCommand=norm -m - convert.vcf
+##bcftools_annotateVersion=1.2+htslib-1.2.1
+##bcftools_annotateCommand=annotate -x FORMAT,QUAL
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA00001	NA00002	NA00003	NA00004	NA00005	NA00006	NA00007	NA00008	NA00009	NA00010
+X	2698560	.	G	A	.	.	.	GT	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0
+X	2698630	.	A	G	.	.	.	GT	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0
+X	2698758	.	CAA	C	.	.	.	GT	0|0	0|1	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0
+X	2698769	.	AAG	A	.	.	.	GT	1|0	1|1	0|1	1|0	1|0	0|0	0|0	0|0	0|0	0|0
+X	2698770	.	AG	A	.	.	.	GT	0|0	0|1	0|0	0|0	1|0	0|0	0|0	0|0	0|0	0|0
+X	2698770	.	AG	AAGG	.	.	.	GT	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0
+X	2698789	.	C	G	.	.	.	GT	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0
+X	2698822	.	A	C	.	.	.	GT	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0
+X	2698831	.	G	A	.	.	.	GT	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0
+X	2698889	.	T	C	.	.	.	GT	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0
+X	2698923	.	G	A	.	.	.	GT	1|0	0|1	0|1	1|0	1|0	0|0	0|0	0|0	0|0	0|0
+X	2698953	.	A	AGG	.	.	.	GT	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0
+X	2698954	.	G	A	.	.	.	GT	1|0	1|1	0|1	1|0	1|0	0|0	0|0	0|1	0|0	0|0
+X	2699002	.	C	A	.	.	.	GT	0|0	0|0	.|.	0|0	0|0	0|0	0|0	0|0	0|0	0|0
+X	2699025	.	T	C	.	.	.	GT	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0
+X	2699091	.	G	A	.	.	.	GT	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0
+X	2699187	.	T	C	.	.	.	GT	0|0	0|0	1|0	0|0	0|1	1|0	1|0	0|0	0|0	0/1
+X	2699188	.	G	C	.	.	.	GT	0|0	0|0	1|0	0|0	0|1	1|0	1|0	0|0	0|0	0|1
+X	2699189	.	T	C	.	.	.	GT	0|0	0|0	1|0	0|0	0|1	1|0	1|0	0|0	0|0	0|1
+X	2699217	.	C	T	.	.	.	GT	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0
+X	2699246	.	C	A	.	.	.	GT	1|0	1|1	0|1	1|1	1|0	0|1	0|0	0|1	0|0	1|0
+X	2699275	.	T	G	.	.	.	GT	0|0	0|0	1|0	0|0	0|1	1|1	1|0	0|0	0|0	0|1
+X	2699350	.	A	T	.	.	.	GT	0|0	0|0	1|0	0|0	0|1	1|0	1|0	0|0	0|0	0|1
+X	2699360	.	T	C	.	.	.	GT	0|0	0|0	1|0	0|0	0|1	1|0	1|0	0|0	0|0	0|1
+X	2699450	.	A	C	.	.	.	GT	0|0	0|0	1|0	0|0	0|1	1|0	1|0	0|0	0|0	0|1
+X	2699507	.	T	C	.	.	.	GT	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0
+X	2699555	.	C	A	.	.	.	GT	0	1	1	0	1	1|1	1|0	0|1	0|0	0|1
+X	2699645	.	G	T	.	.	.	GT	0	1	0	0	0	0|0	0|0	0|1	0|0	0|0
+X	2699676	.	G	A	.	.	.	GT	0	0	1	0	1	1|0	1|0	0|0	0|0	0|1
+X	2699728	.	C	T	.	.	.	GT	0	0	0	0	0	0|0	0|0	0|0	0|0	0|0
+X	2699775	.	C	A	.	.	.	GT	0	0	0	0	0	0|0	0|0	0|0	0|0	0|0
+X	2699898	.	C	CT	.	.	.	GT	0	0	1	0	1	1|0	1|0	0|0	0|0	0|1
+X	2699968	.	A	G	.	.	.	GT	.	0	0	1	0	0|1	0|0	0|0	0|1	1|0
+X	2699970	.	T	C	.	.	.	GT	0	0	0	0	0	0|0	0|0	0|0	0|0	0|0
diff --git a/test/convert.gvcf.out b/test/convert.gvcf.out
index f86e74d..d2c0fc9 100644
--- a/test/convert.gvcf.out
+++ b/test/convert.gvcf.out
@@ -22,38 +22,36 @@
 ##FILTER=<ID=HighSNVSB,Description="SNV strand bias value (SNVSB) exceeds 10">
 ##FILTER=<ID=HighREFREP,Description="Locus contains an indel allele occurring in a homopolymer or dinucleotide track with a reference repeat greater than 8">
 ##FILTER=<ID=HighDepth,Description="Locus depth is greater than 3x the mean chromosome depth">
-##reference=file:///illumina/scripts/clia/Genomes/Homo_sapiens/UCSC/hg19_rCRS/Sequence/WholeGenomeFasta/genome.fa
-##contig=<ID=chr22,length=51304566>
+##contig=<ID=22,length=450>
 ##SnvTheta=0.001
 ##IndelTheta=0.0001
-##MaxDepth_chr1=114.18
-##MaxDepth_chr10=131.73
-##MaxDepth_chr11=117.27
-##MaxDepth_chr12=116.97
-##MaxDepth_chr13=102.24
-##MaxDepth_chr14=101.55
-##MaxDepth_chr15=95.22
-##MaxDepth_chr16=111.33
-##MaxDepth_chr17=112.59
-##MaxDepth_chr18=121.86
-##MaxDepth_chr19=111.12
-##MaxDepth_chr2=121.83
-##MaxDepth_chr20=111.24
-##MaxDepth_chr21=98.43
-##MaxDepth_chr22=76.23
-##MaxDepth_chr3=120.09
-##MaxDepth_chr4=124.50
-##MaxDepth_chr5=119.82
-##MaxDepth_chr6=122.22
-##MaxDepth_chr7=120.27
-##MaxDepth_chr8=120.45
-##MaxDepth_chr9=102.48
-##MaxDepth_chrM=7005.66
-##MaxDepth_chrX=61.05
-##MaxDepth_chrY=37.17
+##MaxDepth_1=114.18
+##MaxDepth_10=131.73
+##MaxDepth_11=117.27
+##MaxDepth_12=116.97
+##MaxDepth_13=102.24
+##MaxDepth_14=101.55
+##MaxDepth_15=95.22
+##MaxDepth_16=111.33
+##MaxDepth_17=112.59
+##MaxDepth_18=121.86
+##MaxDepth_19=111.12
+##MaxDepth_2=121.83
+##MaxDepth_20=111.24
+##MaxDepth_21=98.43
+##MaxDepth_22=76.23
+##MaxDepth_3=120.09
+##MaxDepth_4=124.50
+##MaxDepth_5=119.82
+##MaxDepth_6=122.22
+##MaxDepth_7=120.27
+##MaxDepth_8=120.45
+##MaxDepth_9=102.48
+##MaxDepth_M=7005.66
+##MaxDepth_X=61.05
+##MaxDepth_Y=37.17
 ##FILTER=<ID=IndelSizeFilter,Description="Indel is outside reportable size range. Insertion range: [1,3], Deletion range: [1,11]">
 ##gvcftools_version="0.16"
-##gvcftools_cmdline="/illumina/scripts/clia/workflows/IsisWorkflow/IsisWorkflow_v2.0.13/bin/set_haploid_region --ref /illumina/scripts/clia/Genomes/Homo_sapiens/UCSC/hg19_rCRS/Sequence/WholeGenomeFasta/genome.fa --region-file /illumina/scripts/clia/workflows/IsisWorkflow/IsisWorkflow_v2.0.13/bin/../data/het_mask/ncbi37/male.bed"
 ##FILTER=<ID=HAPLOID_CONFLICT,Description="Locus has heterozygous genotype in a haploid region.">
 ##FORMAT=<ID=OPL,Number=.,Type=Integer,Description="Original PL value before ploidy correction">
 ##INFO=<ID=phastCons,Number=0,Type=Flag,Description="overlaps a phastCons element">
@@ -74,341 +72,337 @@
 ##INFO=<ID=CLNDSDBID,Number=.,Type=String,Description="Colon-delimited list of variant disease database identifier(s). Multiple values from a single database are pipe-delimited">
 ##INFO=<ID=CSQ,Number=A,Type=String,Description="Consequence type as predicted by VEP. Format: Allele|Gene|Feature|Feature_type|Consequence|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|EXON|INTRON|HGNC|MOTIF_NAME|MOTIF_POS|HIGH_INF_POS|MOTIF_SCORE_CHANGE|DISTANCE|CANONICAL|SIFT|PolyPhen|GMAF|ENSP|DOMAINS|CCDS|HGVSc|HGVSp|CELL_TYPE">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	SAMPLE99
-chr22	1	.	N	.	0	LowGQX	END=16050039;BLOCKAVG_min30p3a	GT:GQX:DP:DPF	.:.:0:0
-chr22	16050040	.	C	.	0	LowGQX	END=16050050;BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:5:2:0
-chr22	16050051	.	C	.	0	LowGQX	END=16050056;BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:10:4:0
-chr22	16050057	.	C	.	0	LowGQX	END=16050072;BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:15:6:0
-chr22	16050073	.	G	.	0	LowGQX	END=16050080;BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:21:8:0
-chr22	16050081	.	C	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:30:11:0
-chr22	16050082	.	C	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:30:11:0
-chr22	16050083	.	C	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:30:11:0
-chr22	16050084	.	C	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:30:11:0
-chr22	16050085	.	C	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:30:11:0
-chr22	16050086	.	C	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:30:11:0
-chr22	16050086	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:42:15:0
-chr22	16050087	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:42:15:0
-chr22	16050088	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:42:15:0
-chr22	16050089	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:42:15:0
-chr22	16050090	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:42:15:0
-chr22	16050091	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:42:15:0
-chr22	16050092	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:42:15:0
-chr22	16050093	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:42:15:0
-chr22	16050094	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:42:15:0
-chr22	16050095	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:42:15:0
-chr22	16050096	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:42:15:0
-chr22	16050097	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:42:15:0
-chr22	16050098	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:42:15:0
-chr22	16050099	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:42:15:0
-chr22	16050100	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:42:15:0
-chr22	16050101	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:42:15:0
-chr22	16050102	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:42:15:0
-chr22	16050103	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:42:15:0
-chr22	16050103	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:54:19:0
-chr22	16050104	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:54:19:0
-chr22	16050105	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:54:19:0
-chr22	16050106	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:54:19:0
-chr22	16050107	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:54:19:0
-chr22	16050108	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:54:19:0
-chr22	16050109	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:54:19:0
-chr22	16050110	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:54:19:0
-chr22	16050111	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:54:19:0
-chr22	16050112	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:54:19:0
-chr22	16050113	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:54:19:0
-chr22	16050114	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:54:19:0
-chr22	16050115	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:54:19:0
-chr22	16050116	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:54:19:0
-chr22	16050116	.	G	C	23	LowGQX	SNVSB=0;SNVHPOL=2	GT:GQ:GQX:DP:DPF:AD	0/1:56:23:22:0:16,6
-chr22	16050117	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:69:24:0
-chr22	16050118	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:69:24:0
-chr22	16050119	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:69:24:0
-chr22	16050120	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:69:24:0
-chr22	16050121	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:69:24:0
-chr22	16050122	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:69:24:0
-chr22	16050123	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:69:24:0
-chr22	16050124	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:69:24:0
-chr22	16050125	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:69:24:0
-chr22	16050126	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:69:24:0
-chr22	16050127	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:69:24:0
-chr22	16050128	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:69:24:0
-chr22	16050129	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:69:24:0
-chr22	16050130	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:69:24:0
-chr22	16050131	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:69:24:0
-chr22	16050132	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:69:24:0
-chr22	16050132	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:84:29:0
-chr22	16050133	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:84:29:0
-chr22	16050134	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:84:29:0
-chr22	16050135	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:84:29:0
-chr22	16050136	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:84:29:0
-chr22	16050137	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:84:29:0
-chr22	16050138	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:84:29:0
-chr22	16050139	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:84:29:0
-chr22	16050140	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:84:29:0
-chr22	16050141	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:84:29:0
-chr22	16050142	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:84:29:0
-chr22	16050143	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:84:29:0
-chr22	16050144	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:84:29:0
-chr22	16050145	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:84:29:0
-chr22	16050146	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:84:29:0
-chr22	16050147	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:84:29:0
-chr22	16050148	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:84:29:0
-chr22	16050149	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:84:29:0
-chr22	16050150	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:84:29:0
-chr22	16050151	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:84:29:0
-chr22	16050152	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:84:29:0
-chr22	16050153	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:84:29:0
-chr22	16050154	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:84:29:0
-chr22	16050155	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:84:29:0
-chr22	16050156	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:84:29:0
-chr22	16050157	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:84:29:0
-chr22	16050158	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:84:29:0
-chr22	16050159	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:84:29:0
-chr22	16050160	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:84:29:0
-chr22	16050161	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:84:29:0
-chr22	16050162	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:84:29:0
-chr22	16050163	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:84:29:0
-chr22	16050164	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:84:29:0
-chr22	16050165	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:84:29:0
-chr22	16050166	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:84:29:0
-chr22	16050167	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:84:29:0
-chr22	16050168	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:84:29:0
-chr22	16050169	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:84:29:0
-chr22	16050170	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:84:29:0
-chr22	16050171	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:84:29:0
-chr22	16050171	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:90:31:0
-chr22	16050172	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:90:31:0
-chr22	16050173	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:90:31:0
-chr22	16050174	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:90:31:0
-chr22	16050175	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:90:31:0
-chr22	16050176	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:90:31:0
-chr22	16050177	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:90:31:0
-chr22	16050178	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:90:31:0
-chr22	16050179	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:90:31:0
-chr22	16050180	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:90:31:0
-chr22	16050181	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:90:31:0
-chr22	16050182	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:90:31:0
-chr22	16050183	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:90:31:0
-chr22	16050184	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:90:31:0
-chr22	16050185	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:90:31:0
-chr22	16050186	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:90:31:0
-chr22	16050187	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:90:31:0
-chr22	16050188	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:90:31:0
-chr22	16050189	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:90:31:0
-chr22	16050190	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:90:31:0
-chr22	16050191	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:90:31:0
-chr22	16050192	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:90:31:0
-chr22	16050193	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:90:31:0
-chr22	16050194	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:90:31:0
-chr22	16050195	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:90:31:0
-chr22	16050196	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:90:31:0
-chr22	16050197	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:90:31:0
-chr22	16050198	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:90:31:0
-chr22	16050199	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:90:31:0
-chr22	16050200	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:90:31:0
-chr22	16050201	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:90:31:0
-chr22	16050202	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:90:31:0
-chr22	16050203	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:90:31:0
-chr22	16050204	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:90:31:0
-chr22	16050205	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:90:31:0
-chr22	16050206	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:90:31:0
-chr22	16050207	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:90:31:0
-chr22	16050208	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:90:31:0
-chr22	16050209	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:90:31:0
-chr22	16050210	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:90:31:0
-chr22	16050211	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:90:31:0
-chr22	16050212	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:90:31:0
-chr22	16050213	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:90:31:0
-chr22	16050214	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:90:31:0
-chr22	16050215	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:90:31:0
-chr22	16050216	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:90:31:0
-chr22	16050216	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:93:32:2
-chr22	16050217	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:93:32:2
-chr22	16050218	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:93:32:2
-chr22	16050218	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:102:35:0
-chr22	16050219	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:102:35:0
-chr22	16050220	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:102:35:0
-chr22	16050221	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:102:35:0
-chr22	16050222	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:102:35:0
-chr22	16050223	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:102:35:0
-chr22	16050224	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:102:35:0
-chr22	16050225	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:102:35:0
-chr22	16050226	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:102:35:0
-chr22	16050227	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:102:35:0
-chr22	16050228	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:102:35:0
-chr22	16050229	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:102:35:0
-chr22	16050230	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:102:35:0
-chr22	16050231	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:102:35:0
-chr22	16050232	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:102:35:0
-chr22	16050233	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:102:35:0
-chr22	16050234	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:102:35:0
-chr22	16050235	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:102:35:0
-chr22	16050235	.	T	.	0	PASS	.	GT:GQX:DP:DPF	0/0:72:36:0
-chr22	16050236	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:87:30:0
-chr22	16050237	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:87:30:0
-chr22	16050238	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:87:30:0
-chr22	16050239	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:87:30:0
-chr22	16050240	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:87:30:0
-chr22	16050241	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:87:30:0
-chr22	16050242	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:87:30:0
-chr22	16050243	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:87:30:0
-chr22	16050244	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:87:30:0
-chr22	16050245	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:87:30:0
-chr22	16050246	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:87:30:0
-chr22	16050247	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:87:30:0
-chr22	16050248	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:87:30:0
-chr22	16050249	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:87:30:0
-chr22	16050250	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:87:30:0
-chr22	16050251	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:87:30:0
-chr22	16050252	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:87:30:0
-chr22	16050253	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:87:30:0
-chr22	16050254	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:87:30:0
-chr22	16050255	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:87:30:0
-chr22	16050256	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:87:30:0
-chr22	16050257	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:87:30:0
-chr22	16050258	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:87:30:0
-chr22	16050259	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:87:30:0
-chr22	16050260	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:87:30:0
-chr22	16050261	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:87:30:0
-chr22	16050262	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:87:30:0
-chr22	16050262	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:66:23:0
-chr22	16050263	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:66:23:0
-chr22	16050264	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:66:23:0
-chr22	16050265	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:66:23:0
-chr22	16050266	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:66:23:0
-chr22	16050267	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:66:23:0
-chr22	16050268	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:66:23:0
-chr22	16050269	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:66:23:0
-chr22	16050270	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:66:23:0
-chr22	16050271	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:66:23:0
-chr22	16050272	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:66:23:0
-chr22	16050273	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:66:23:0
-chr22	16050274	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:66:23:0
-chr22	16050275	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:66:23:0
-chr22	16050276	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:66:23:0
-chr22	16050277	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:66:23:0
-chr22	16050278	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:66:23:0
-chr22	16050279	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:66:23:0
-chr22	16050280	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:66:23:0
-chr22	16050280	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:87:30:0
-chr22	16050281	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:87:30:0
-chr22	16050282	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:87:30:0
-chr22	16050283	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:87:30:0
-chr22	16050284	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:87:30:0
-chr22	16050285	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:87:30:0
-chr22	16050286	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:87:30:0
-chr22	16050287	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:87:30:0
-chr22	16050288	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:87:30:0
-chr22	16050288	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:114:39:0
-chr22	16050289	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:114:39:0
-chr22	16050290	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:114:39:0
-chr22	16050291	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:114:39:0
-chr22	16050292	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:114:39:0
-chr22	16050293	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:114:39:0
-chr22	16050294	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:114:39:0
-chr22	16050295	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:114:39:0
-chr22	16050296	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:114:39:0
-chr22	16050297	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:114:39:0
-chr22	16050298	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:114:39:0
-chr22	16050299	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:114:39:0
-chr22	16050300	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:114:39:0
-chr22	16050300	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:150:51:0
-chr22	16050301	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:150:51:0
-chr22	16050302	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:150:51:0
-chr22	16050303	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:150:51:0
-chr22	16050304	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:150:51:0
-chr22	16050305	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:150:51:0
-chr22	16050306	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:150:51:0
-chr22	16050307	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:150:51:0
-chr22	16050308	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:150:51:0
-chr22	16050309	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:150:51:0
-chr22	16050310	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:150:51:0
-chr22	16050310	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:166:63:0
-chr22	16050311	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:166:63:0
-chr22	16050312	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:166:63:0
-chr22	16050313	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:166:63:0
-chr22	16050314	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:166:63:0
-chr22	16050315	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:166:63:0
-chr22	16050316	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:166:63:0
-chr22	16050317	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:166:63:0
-chr22	16050318	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:166:63:0
-chr22	16050319	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:166:63:0
-chr22	16050320	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:166:63:0
-chr22	16050321	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:166:63:0
-chr22	16050322	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:166:63:0
-chr22	16050323	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:166:63:0
-chr22	16050324	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:166:63:0
-chr22	16050325	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:166:63:0
-chr22	16050326	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:166:63:0
-chr22	16050327	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:166:63:0
-chr22	16050328	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:166:63:0
-chr22	16050329	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:166:63:0
-chr22	16050330	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:166:63:0
-chr22	16050331	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:166:63:0
-chr22	16050332	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:166:63:0
-chr22	16050333	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:166:63:0
-chr22	16050334	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:166:63:0
-chr22	16050335	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:166:63:0
-chr22	16050336	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:166:63:0
-chr22	16050337	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:166:63:0
-chr22	16050338	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:166:63:0
-chr22	16050339	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:166:63:0
-chr22	16050340	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:166:63:0
-chr22	16050341	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:166:63:0
-chr22	16050342	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:166:63:0
-chr22	16050343	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:166:63:0
-chr22	16050344	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:166:63:0
-chr22	16050345	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:166:63:0
-chr22	16050345	.	C	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:220:74:0
-chr22	16050346	.	C	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:220:74:0
-chr22	16050347	.	C	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:220:74:0
-chr22	16050347	.	T	.	0	HighDepth	END=16050372;BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:229:77:0
-chr22	16050373	.	T	.	0	HighDepth	END=16050407;BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:241:81:0
-chr22	16050408	.	T	.	0	HighDepth	END=16050414;BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:200:75:0
-chr22	16050415	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:217:73:0
-chr22	16050416	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:217:73:0
-chr22	16050417	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:217:73:0
-chr22	16050418	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:217:73:0
-chr22	16050419	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:217:73:0
-chr22	16050419	.	C	.	0	HighDepth	END=16050420;BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:223:75:0
-chr22	16050421	.	T	.	0	PASS	.	GT:GQX:DP:DPF	0/0:223:75:1
-chr22	16050422	.	T	.	0	HighDepth	END=16050427;BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:223:75:0
-chr22	16050428	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:178:60:0
-chr22	16050429	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:178:60:0
-chr22	16050430	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:178:60:0
-chr22	16050431	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:178:60:0
-chr22	16050432	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:178:60:0
-chr22	16050433	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:178:60:0
-chr22	16050434	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:178:60:0
-chr22	16050435	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:178:60:0
-chr22	16050436	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:178:60:0
-chr22	16050437	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:178:60:0
-chr22	16050438	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:178:60:0
-chr22	16050439	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:178:60:0
-chr22	16050440	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:178:60:0
-chr22	16050441	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:178:60:0
-chr22	16050442	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:178:60:0
-chr22	16050443	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:178:60:0
-chr22	16050444	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:178:60:0
-chr22	16050445	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:178:60:0
-chr22	16050446	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:178:60:0
-chr22	16050447	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:178:60:0
-chr22	16050448	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:178:60:0
-chr22	16050449	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:178:60:0
-chr22	16050450	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:178:60:0
-chr22	16050451	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:178:60:0
-chr22	16050451	.	C	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:142:54:0
-chr22	16050452	.	C	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:142:54:0
-chr22	16050453	.	C	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:142:54:0
-chr22	16050454	.	C	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:142:54:0
-chr22	16050455	.	C	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:142:54:0
-chr22	16050456	.	C	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:142:54:0
-chr22	16050457	.	C	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:142:54:0
-chr22	16050458	.	C	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:142:54:0
-chr22	16050459	.	C	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:142:54:0
-chr22	16050460	.	C	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:142:54:0
-chr22	16050461	.	C	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:142:54:0
-chr22	16050462	.	C	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:142:54:0
-chr22	16050463	.	C	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:142:54:0
-chr22	16050464	.	C	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:142:54:0
-chr22	16050465	.	C	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:142:54:0
-chr22	16050466	.	C	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:142:54:0
-chr22	16050467	.	C	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:142:54:0
+22	1	.	N	.	0	LowGQX	END=9;BLOCKAVG_min30p3a	GT:GQX:DP:DPF	.:.:0:0
+22	10	.	C	.	0	LowGQX	END=20;BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:5:2:0
+22	21	.	C	.	0	LowGQX	END=26;BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:10:4:0
+22	27	.	C	.	0	LowGQX	END=42;BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:15:6:0
+22	43	.	G	.	0	LowGQX	END=50;BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:21:8:0
+22	51	.	C	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:30:11:0
+22	52	.	C	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:30:11:0
+22	53	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:30:11:0
+22	54	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:30:11:0
+22	55	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:30:11:0
+22	56	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:42:15:0
+22	57	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:42:15:0
+22	58	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:42:15:0
+22	59	.	C	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:42:15:0
+22	60	.	C	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:42:15:0
+22	61	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:42:15:0
+22	62	.	C	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:42:15:0
+22	63	.	C	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:42:15:0
+22	64	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:42:15:0
+22	65	.	C	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:42:15:0
+22	66	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:42:15:0
+22	67	.	C	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:42:15:0
+22	68	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:42:15:0
+22	69	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:42:15:0
+22	70	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:42:15:0
+22	71	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:42:15:0
+22	72	.	C	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:42:15:0
+22	73	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:54:19:0
+22	74	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:54:19:0
+22	75	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:54:19:0
+22	76	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:54:19:0
+22	77	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:54:19:0
+22	78	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:54:19:0
+22	79	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:54:19:0
+22	80	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:54:19:0
+22	81	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:54:19:0
+22	82	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:54:19:0
+22	83	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:54:19:0
+22	84	.	C	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:54:19:0
+22	85	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:54:19:0
+22	86	.	G	C	23	LowGQX	SNVSB=0;SNVHPOL=2	GT:GQ:GQX:DP:DPF:AD	0/1:56:23:22:0:16,6
+22	87	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:69:24:0
+22	88	.	C	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:69:24:0
+22	89	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:69:24:0
+22	90	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:69:24:0
+22	91	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:69:24:0
+22	92	.	C	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:69:24:0
+22	93	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:69:24:0
+22	94	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:69:24:0
+22	95	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:69:24:0
+22	96	.	C	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:69:24:0
+22	97	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:69:24:0
+22	98	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:69:24:0
+22	99	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:69:24:0
+22	100	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:69:24:0
+22	101	.	C	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:69:24:0
+22	102	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:84:29:0
+22	103	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:84:29:0
+22	104	.	C	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:84:29:0
+22	105	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:84:29:0
+22	106	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:84:29:0
+22	107	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:84:29:0
+22	108	.	C	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:84:29:0
+22	109	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:84:29:0
+22	110	.	C	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:84:29:0
+22	111	.	C	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:84:29:0
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+22	113	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:84:29:0
+22	114	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:84:29:0
+22	115	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:84:29:0
+22	116	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:84:29:0
+22	117	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:84:29:0
+22	118	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:84:29:0
+22	119	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:84:29:0
+22	120	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:84:29:0
+22	121	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:84:29:0
+22	122	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:84:29:0
+22	123	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:84:29:0
+22	124	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:84:29:0
+22	125	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:84:29:0
+22	126	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:84:29:0
+22	127	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:84:29:0
+22	128	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:84:29:0
+22	129	.	C	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:84:29:0
+22	130	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:84:29:0
+22	131	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:84:29:0
+22	132	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:84:29:0
+22	133	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:84:29:0
+22	134	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:84:29:0
+22	135	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:84:29:0
+22	136	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:84:29:0
+22	137	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:84:29:0
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+22	139	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:84:29:0
+22	140	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:84:29:0
+22	141	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:90:31:0
+22	142	.	C	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:90:31:0
+22	143	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:90:31:0
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+22	145	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:90:31:0
+22	146	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:90:31:0
+22	147	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:90:31:0
+22	148	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:90:31:0
+22	149	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:90:31:0
+22	150	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:90:31:0
+22	151	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:90:31:0
+22	152	.	C	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:90:31:0
+22	153	.	C	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:90:31:0
+22	154	.	C	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:90:31:0
+22	155	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:90:31:0
+22	156	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:90:31:0
+22	157	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:90:31:0
+22	158	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:90:31:0
+22	159	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:90:31:0
+22	160	.	C	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:90:31:0
+22	161	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:90:31:0
+22	162	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:90:31:0
+22	163	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:90:31:0
+22	164	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:90:31:0
+22	165	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:90:31:0
+22	166	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:90:31:0
+22	167	.	C	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:90:31:0
+22	168	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:90:31:0
+22	169	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:90:31:0
+22	170	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:90:31:0
+22	171	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:90:31:0
+22	172	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:90:31:0
+22	173	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:90:31:0
+22	174	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:90:31:0
+22	175	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:90:31:0
+22	176	.	C	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:90:31:0
+22	177	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:90:31:0
+22	178	.	C	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:90:31:0
+22	179	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:90:31:0
+22	180	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:90:31:0
+22	181	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:90:31:0
+22	182	.	C	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:90:31:0
+22	183	.	C	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:90:31:0
+22	184	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:90:31:0
+22	185	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:90:31:0
+22	186	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:93:32:2
+22	187	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:93:32:2
+22	188	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:102:35:0
+22	189	.	C	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:102:35:0
+22	190	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:102:35:0
+22	191	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:102:35:0
+22	192	.	C	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:102:35:0
+22	193	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:102:35:0
+22	194	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:102:35:0
+22	195	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:102:35:0
+22	196	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:102:35:0
+22	197	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:102:35:0
+22	198	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:102:35:0
+22	199	.	C	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:102:35:0
+22	200	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:102:35:0
+22	201	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:102:35:0
+22	202	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:102:35:0
+22	203	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:102:35:0
+22	204	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:102:35:0
+22	205	.	T	.	0	PASS	.	GT:GQX:DP:DPF	0/0:72:36:0
+22	206	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:87:30:0
+22	207	.	C	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:87:30:0
+22	208	.	C	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:87:30:0
+22	209	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:87:30:0
+22	210	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:87:30:0
+22	211	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:87:30:0
+22	212	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:87:30:0
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+22	214	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:87:30:0
+22	215	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:87:30:0
+22	216	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:87:30:0
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+22	218	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:87:30:0
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+22	220	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:87:30:0
+22	221	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:87:30:0
+22	222	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:87:30:0
+22	223	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:87:30:0
+22	224	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:87:30:0
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+22	226	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:87:30:0
+22	227	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:87:30:0
+22	228	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:87:30:0
+22	229	.	C	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:87:30:0
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+22	231	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:87:30:0
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+22	233	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:66:23:0
+22	234	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:66:23:0
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+22	236	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:66:23:0
+22	237	.	C	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:66:23:0
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+22	249	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:66:23:0
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+22	251	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:87:30:0
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+22	269	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:114:39:0
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+22	271	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:150:51:0
+22	272	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:150:51:0
+22	273	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:150:51:0
+22	274	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:150:51:0
+22	275	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:150:51:0
+22	276	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:150:51:0
+22	277	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:150:51:0
+22	278	.	C	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:150:51:0
+22	279	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:150:51:0
+22	280	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:166:63:0
+22	281	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:166:63:0
+22	282	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:166:63:0
+22	283	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:166:63:0
+22	284	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:166:63:0
+22	285	.	C	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:166:63:0
+22	286	.	C	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:166:63:0
+22	287	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:166:63:0
+22	288	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:166:63:0
+22	289	.	C	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:166:63:0
+22	290	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:166:63:0
+22	291	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:166:63:0
+22	292	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:166:63:0
+22	293	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:166:63:0
+22	294	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:166:63:0
+22	295	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:166:63:0
+22	296	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:166:63:0
+22	297	.	C	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:166:63:0
+22	298	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:166:63:0
+22	299	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:166:63:0
+22	300	.	C	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:166:63:0
+22	301	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:166:63:0
+22	302	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:166:63:0
+22	303	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:166:63:0
+22	304	.	C	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:166:63:0
+22	305	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:166:63:0
+22	306	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:166:63:0
+22	307	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:166:63:0
+22	308	.	C	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:166:63:0
+22	309	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:166:63:0
+22	310	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:166:63:0
+22	311	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:166:63:0
+22	312	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:166:63:0
+22	313	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:166:63:0
+22	314	.	C	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:166:63:0
+22	315	.	C	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:220:74:0
+22	316	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:220:74:0
+22	317	.	T	.	0	HighDepth	END=342;BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:229:77:0
+22	343	.	T	.	0	HighDepth	END=377;BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:241:81:0
+22	378	.	T	.	0	HighDepth	END=384;BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:200:75:0
+22	385	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:217:73:0
+22	386	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:217:73:0
+22	387	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:217:73:0
+22	388	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:217:73:0
+22	389	.	C	.	0	HighDepth	END=390;BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:223:75:0
+22	391	.	T	.	0	PASS	.	GT:GQX:DP:DPF	0/0:223:75:1
+22	392	.	T	.	0	HighDepth	END=397;BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:223:75:0
+22	398	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:178:60:0
+22	399	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:178:60:0
+22	400	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:178:60:0
+22	401	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:178:60:0
+22	402	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:178:60:0
+22	403	.	C	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:178:60:0
+22	404	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:178:60:0
+22	405	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:178:60:0
+22	406	.	C	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:178:60:0
+22	407	.	C	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:178:60:0
+22	408	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:178:60:0
+22	409	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:178:60:0
+22	410	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:178:60:0
+22	411	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:178:60:0
+22	412	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:178:60:0
+22	413	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:178:60:0
+22	414	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:178:60:0
+22	415	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:178:60:0
+22	416	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:178:60:0
+22	417	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:178:60:0
+22	418	.	C	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:178:60:0
+22	419	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:178:60:0
+22	420	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:178:60:0
+22	421	.	C	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:142:54:0
+22	422	.	C	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:142:54:0
+22	423	.	C	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:142:54:0
+22	424	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:142:54:0
+22	425	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:142:54:0
+22	426	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:142:54:0
+22	427	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:142:54:0
+22	428	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:142:54:0
+22	429	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:142:54:0
+22	430	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:142:54:0
+22	431	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:142:54:0
+22	432	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:142:54:0
+22	433	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:142:54:0
+22	434	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:142:54:0
+22	435	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:142:54:0
+22	436	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:142:54:0
+22	437	.	C	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:142:54:0
+22	438	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:142:54:0
+22	439	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:142:54:0
+22	440	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:142:54:0
+22	441	.	C	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:142:54:0
+22	442	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:142:54:0
+22	443	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:142:54:0
+22	444	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:142:54:0
+22	445	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:142:54:0
+22	446	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:142:54:0
+22	447	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:142:54:0
+22	448	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:142:54:0
+22	449	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:142:54:0
+22	450	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:142:54:0
diff --git a/test/convert.gvcf.vcf b/test/convert.gvcf.vcf
index 402d57f..6dfc44d 100644
--- a/test/convert.gvcf.vcf
+++ b/test/convert.gvcf.vcf
@@ -22,38 +22,36 @@
 ##FILTER=<ID=HighSNVSB,Description="SNV strand bias value (SNVSB) exceeds 10">
 ##FILTER=<ID=HighREFREP,Description="Locus contains an indel allele occurring in a homopolymer or dinucleotide track with a reference repeat greater than 8">
 ##FILTER=<ID=HighDepth,Description="Locus depth is greater than 3x the mean chromosome depth">
-##reference=file:///illumina/scripts/clia/Genomes/Homo_sapiens/UCSC/hg19_rCRS/Sequence/WholeGenomeFasta/genome.fa
-##contig=<ID=chr22,length=51304566>
+##contig=<ID=22,length=450>
 ##SnvTheta=0.001
 ##IndelTheta=0.0001
-##MaxDepth_chr1=114.18
-##MaxDepth_chr10=131.73
-##MaxDepth_chr11=117.27
-##MaxDepth_chr12=116.97
-##MaxDepth_chr13=102.24
-##MaxDepth_chr14=101.55
-##MaxDepth_chr15=95.22
-##MaxDepth_chr16=111.33
-##MaxDepth_chr17=112.59
-##MaxDepth_chr18=121.86
-##MaxDepth_chr19=111.12
-##MaxDepth_chr2=121.83
-##MaxDepth_chr20=111.24
-##MaxDepth_chr21=98.43
-##MaxDepth_chr22=76.23
-##MaxDepth_chr3=120.09
-##MaxDepth_chr4=124.50
-##MaxDepth_chr5=119.82
-##MaxDepth_chr6=122.22
-##MaxDepth_chr7=120.27
-##MaxDepth_chr8=120.45
-##MaxDepth_chr9=102.48
-##MaxDepth_chrM=7005.66
-##MaxDepth_chrX=61.05
-##MaxDepth_chrY=37.17
+##MaxDepth_1=114.18
+##MaxDepth_10=131.73
+##MaxDepth_11=117.27
+##MaxDepth_12=116.97
+##MaxDepth_13=102.24
+##MaxDepth_14=101.55
+##MaxDepth_15=95.22
+##MaxDepth_16=111.33
+##MaxDepth_17=112.59
+##MaxDepth_18=121.86
+##MaxDepth_19=111.12
+##MaxDepth_2=121.83
+##MaxDepth_20=111.24
+##MaxDepth_21=98.43
+##MaxDepth_22=76.23
+##MaxDepth_3=120.09
+##MaxDepth_4=124.50
+##MaxDepth_5=119.82
+##MaxDepth_6=122.22
+##MaxDepth_7=120.27
+##MaxDepth_8=120.45
+##MaxDepth_9=102.48
+##MaxDepth_M=7005.66
+##MaxDepth_X=61.05
+##MaxDepth_Y=37.17
 ##FILTER=<ID=IndelSizeFilter,Description="Indel is outside reportable size range. Insertion range: [1,3], Deletion range: [1,11]">
 ##gvcftools_version="0.16"
-##gvcftools_cmdline="/illumina/scripts/clia/workflows/IsisWorkflow/IsisWorkflow_v2.0.13/bin/set_haploid_region --ref /illumina/scripts/clia/Genomes/Homo_sapiens/UCSC/hg19_rCRS/Sequence/WholeGenomeFasta/genome.fa --region-file /illumina/scripts/clia/workflows/IsisWorkflow/IsisWorkflow_v2.0.13/bin/../data/het_mask/ncbi37/male.bed"
 ##FILTER=<ID=HAPLOID_CONFLICT,Description="Locus has heterozygous genotype in a haploid region.">
 ##FORMAT=<ID=OPL,Number=.,Type=Integer,Description="Original PL value before ploidy correction">
 ##INFO=<ID=phastCons,Number=0,Type=Flag,Description="overlaps a phastCons element">
@@ -74,34 +72,34 @@
 ##INFO=<ID=CLNDSDBID,Number=.,Type=String,Description="Colon-delimited list of variant disease database identifier(s). Multiple values from a single database are pipe-delimited">
 ##INFO=<ID=CSQ,Number=A,Type=String,Description="Consequence type as predicted by VEP. Format: Allele|Gene|Feature|Feature_type|Consequence|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|EXON|INTRON|HGNC|MOTIF_NAME|MOTIF_POS|HIGH_INF_POS|MOTIF_SCORE_CHANGE|DISTANCE|CANONICAL|SIFT|PolyPhen|GMAF|ENSP|DOMAINS|CCDS|HGVSc|HGVSp|CELL_TYPE">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	SAMPLE99
-chr22	1	.	N	.	0	LowGQX	END=16050039;BLOCKAVG_min30p3a	GT:GQX:DP:DPF	.:.:0:0
-chr22	16050040	.	C	.	0	LowGQX	END=16050050;BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:5:2:0
-chr22	16050051	.	C	.	0	LowGQX	END=16050056;BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:10:4:0
-chr22	16050057	.	C	.	0	LowGQX	END=16050072;BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:15:6:0
-chr22	16050073	.	G	.	0	LowGQX	END=16050080;BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:21:8:0
-chr22	16050081	.	C	.	0	PASS	END=16050085;BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:30:11:0
-chr22	16050086	.	G	.	0	PASS	END=16050102;BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:42:15:0
-chr22	16050103	.	T	.	0	PASS	END=16050115;BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:54:19:0
-chr22	16050116	.	G	C	23	LowGQX	SNVSB=0;SNVHPOL=2	GT:GQ:GQX:DP:DPF:AD	0/1:56:23:22:0:16,6
-chr22	16050117	.	T	.	0	PASS	END=16050131;BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:69:24:0
-chr22	16050132	.	A	.	0	PASS	END=16050170;BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:84:29:0
-chr22	16050171	.	G	.	0	PASS	END=16050215;BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:90:31:0
-chr22	16050216	.	T	.	0	PASS	END=16050217;BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:93:32:2
-chr22	16050218	.	T	.	0	PASS	END=16050234;BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:102:35:0
-chr22	16050235	.	T	.	0	PASS	.	GT:GQX:DP:DPF	0/0:72:36:0
-chr22	16050236	.	T	.	0	PASS	END=16050261;BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:87:30:0
-chr22	16050262	.	A	.	0	PASS	END=16050279;BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:66:23:0
-chr22	16050280	.	G	.	0	PASS	END=16050287;BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:87:30:0
-chr22	16050288	.	A	.	0	PASS	END=16050299;BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:114:39:0
-chr22	16050300	.	G	.	0	PASS	END=16050309;BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:150:51:0
-chr22	16050310	.	A	.	0	PASS	END=16050344;BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:166:63:0
-chr22	16050345	.	C	.	0	PASS	END=16050346;BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:220:74:0
-chr22	16050347	.	T	.	0	HighDepth	END=16050372;BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:229:77:0
-chr22	16050373	.	T	.	0	HighDepth	END=16050407;BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:241:81:0
-chr22	16050408	.	T	.	0	HighDepth	END=16050414;BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:200:75:0
-chr22	16050415	.	G	.	0	PASS	END=16050418;BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:217:73:0
-chr22	16050419	.	C	.	0	HighDepth	END=16050420;BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:223:75:0
-chr22	16050421	.	T	.	0	PASS	.	GT:GQX:DP:DPF	0/0:223:75:1
-chr22	16050422	.	T	.	0	HighDepth	END=16050427;BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:223:75:0
-chr22	16050428	.	T	.	0	PASS	END=16050450;BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:178:60:0
-chr22	16050451	.	C	.	0	PASS	END=16050466;BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:142:54:0
+22	1	.	N	.	0	LowGQX	END=9;BLOCKAVG_min30p3a	GT:GQX:DP:DPF	.:.:0:0
+22	10	.	C	.	0	LowGQX	END=20;BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:5:2:0
+22	21	.	C	.	0	LowGQX	END=26;BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:10:4:0
+22	27	.	C	.	0	LowGQX	END=42;BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:15:6:0
+22	43	.	G	.	0	LowGQX	END=50;BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:21:8:0
+22	51	.	C	.	0	PASS	END=55;BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:30:11:0
+22	56	.	G	.	0	PASS	END=72;BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:42:15:0
+22	73	.	T	.	0	PASS	END=85;BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:54:19:0
+22	86	.	G	C	23	LowGQX	SNVSB=0;SNVHPOL=2	GT:GQ:GQX:DP:DPF:AD	0/1:56:23:22:0:16,6
+22	87	.	T	.	0	PASS	END=101;BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:69:24:0
+22	102	.	A	.	0	PASS	END=140;BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:84:29:0
+22	141	.	G	.	0	PASS	END=185;BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:90:31:0
+22	186	.	T	.	0	PASS	END=187;BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:93:32:2
+22	188	.	T	.	0	PASS	END=204;BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:102:35:0
+22	205	.	T	.	0	PASS	.	GT:GQX:DP:DPF	0/0:72:36:0
+22	206	.	T	.	0	PASS	END=231;BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:87:30:0
+22	232	.	A	.	0	PASS	END=249;BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:66:23:0
+22	250	.	G	.	0	PASS	END=257;BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:87:30:0
+22	258	.	A	.	0	PASS	END=269;BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:114:39:0
+22	270	.	G	.	0	PASS	END=279;BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:150:51:0
+22	280	.	A	.	0	PASS	END=314;BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:166:63:0
+22	315	.	C	.	0	PASS	END=316;BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:220:74:0
+22	317	.	T	.	0	HighDepth	END=342;BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:229:77:0
+22	343	.	T	.	0	HighDepth	END=377;BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:241:81:0
+22	378	.	T	.	0	HighDepth	END=384;BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:200:75:0
+22	385	.	G	.	0	PASS	END=388;BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:217:73:0
+22	389	.	C	.	0	HighDepth	END=390;BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:223:75:0
+22	391	.	T	.	0	PASS	.	GT:GQX:DP:DPF	0/0:223:75:1
+22	392	.	T	.	0	HighDepth	END=397;BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:223:75:0
+22	398	.	T	.	0	PASS	END=420;BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:178:60:0
+22	421	.	C	.	0	PASS	END=450;BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:142:54:0
diff --git a/test/convert.hls.gt.hap b/test/convert.hls.gt.hap
new file mode 100644
index 0000000..fe34c30
--- /dev/null
+++ b/test/convert.hls.gt.hap
@@ -0,0 +1,35 @@
+0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
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+0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+1 0 1 1 0 1 1 0 1 0 0 0 0 0 0 1 0 0 0 0
+0 0 0 0 ? ? 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+0 0 0 0 1 0 0 0 0 1 1 0 1 0 0 0 0 0 0* 1*
+0 0 0 0 1 0 0 0 0 1 1 0 1 0 0 0 0 0 0 1
+0 0 0 0 1 0 0 0 0 1 1 0 1 0 0 0 0 0 0 1
+0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+1 0 1 1 0 1 1 1 1 0 0 1 0 0 0 1 0 0 1 0
+0 0 0 0 1 0 0 0 0 1 1 1 1 0 0 0 0 0 0 1
+0 0 0 0 1 0 0 0 0 1 1 0 1 0 0 0 0 0 0 1
+0 0 0 0 1 0 0 0 0 1 1 0 1 0 0 0 0 0 0 1
+0 0 0 0 1 0 0 0 0 1 1 0 1 0 0 0 0 0 0 1
+0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+0 - 1 - 1 - 0 - 1 - 1 1 1 0 0 1 0 0 0 1
+0 - 1 - 0 - 0 - 0 - 0 0 0 0 0 1 0 0 0 0
+0 - 0 - 1 - 0 - 1 - 1 0 1 0 0 0 0 0 0 1
+0 - 0 - 0 - 0 - 0 - 0 0 0 0 0 0 0 0 0 0
+0 - 0 - 0 - 0 - 0 - 0 0 0 0 0 0 0 0 0 0
+0 - 0 - 1 - 0 - 1 - 1 0 1 0 0 0 0 0 0 1
+? - 0 - 0 - 1 - 0 - 0 1 0 0 0 0 0 1 1 0
+0 - 0 - 0 - 0 - 0 - 0 0 0 0 0 0 0 0 0 0
+0 0 0 0 1 0 0 0 0 1 1 0 1 0 0 0 0 0 0 1
diff --git a/test/convert.hls.gt.legend b/test/convert.hls.gt.legend
new file mode 100644
index 0000000..1c88f60
--- /dev/null
+++ b/test/convert.hls.gt.legend
@@ -0,0 +1,36 @@
+id position a0 a1
+X:2698560_G_A 2698560 G A
+X:2698630_A_G 2698630 A G
+X:2698758_CAA_C 2698758 CAA C
+X:2698769_AAG_A 2698769 AAG A
+X:2698770_AG_A 2698770 AG A
+X:2698770_AG_AAGG 2698770 AG AAGG
+X:2698789_C_G 2698789 C G
+X:2698822_A_C 2698822 A C
+X:2698831_G_A 2698831 G A
+X:2698889_T_C 2698889 T C
+X:2698923_G_A 2698923 G A
+X:2698953_A_AGG 2698953 A AGG
+X:2698954_G_A 2698954 G A
+X:2699002_C_A 2699002 C A
+X:2699025_T_C 2699025 T C
+X:2699091_G_A 2699091 G A
+X:2699187_T_C 2699187 T C
+X:2699188_G_C 2699188 G C
+X:2699189_T_C 2699189 T C
+X:2699217_C_T 2699217 C T
+X:2699246_C_A 2699246 C A
+X:2699275_T_G 2699275 T G
+X:2699350_A_T 2699350 A T
+X:2699360_T_C 2699360 T C
+X:2699450_A_C 2699450 A C
+X:2699507_T_C 2699507 T C
+X:2699555_C_A 2699555 C A
+X:2699645_G_T 2699645 G T
+X:2699676_G_A 2699676 G A
+X:2699728_C_T 2699728 C T
+X:2699775_C_A 2699775 C A
+X:2699898_C_CT 2699898 C CT
+X:2699968_A_G 2699968 A G
+X:2699970_T_C 2699970 T C
+X:2699990_C_<INS:ME:LINE1>_2700054 2699990 C <INS:ME:LINE1>
diff --git a/test/convert.hls.gt.samples b/test/convert.hls.gt.samples
new file mode 100644
index 0000000..c1eea1a
--- /dev/null
+++ b/test/convert.hls.gt.samples
@@ -0,0 +1,11 @@
+sample population group sex
+NA00001 NA00001 NA00001 2
+NA00002 NA00002 NA00002 2
+NA00003 NA00003 NA00003 2
+NA00004 NA00004 NA00004 2
+NA00005 NA00005 NA00005 2
+NA00006 NA00006 NA00006 2
+NA00007 NA00007 NA00007 2
+NA00008 NA00008 NA00008 2
+NA00009 NA00009 NA00009 2
+NA00010 NA00010 NA00010 2
diff --git a/test/convert.hs.gt.hap b/test/convert.hs.gt.hap
new file mode 100644
index 0000000..2e41c5c
--- /dev/null
+++ b/test/convert.hs.gt.hap
@@ -0,0 +1,35 @@
+X:2698560_G_A X:2698560_G_A 2698560 G A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+X:2698630_A_G X:2698630_A_G 2698630 A G 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+X:2698758_CAA_C X:2698758_CAA_C 2698758 CAA C 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+X:2698769_AAG_A X:2698769_AAG_A 2698769 AAG A 1 0 1 1 0 1 1 0 1 0 0 0 0 0 0 0 0 0 0 0
+X:2698770_AG_A X:2698770_AG_A 2698770 AG A 0 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0
+X:2698770_AG_AAGG X:2698770_AG_AAGG 2698770 AG AAGG 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+X:2698789_C_G X:2698789_C_G 2698789 C G 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+X:2698822_A_C X:2698822_A_C 2698822 A C 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+X:2698831_G_A X:2698831_G_A 2698831 G A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+X:2698889_T_C X:2698889_T_C 2698889 T C 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+X:2698923_G_A X:2698923_G_A 2698923 G A 1 0 0 1 0 1 1 0 1 0 0 0 0 0 0 0 0 0 0 0
+X:2698953_A_AGG X:2698953_A_AGG 2698953 A AGG 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+X:2698954_G_A X:2698954_G_A 2698954 G A 1 0 1 1 0 1 1 0 1 0 0 0 0 0 0 1 0 0 0 0
+X:2699002_C_A X:2699002_C_A 2699002 C A 0 0 0 0 ? ? 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+X:2699025_T_C X:2699025_T_C 2699025 T C 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+X:2699091_G_A X:2699091_G_A 2699091 G A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+X:2699187_T_C X:2699187_T_C 2699187 T C 0 0 0 0 1 0 0 0 0 1 1 0 1 0 0 0 0 0 0* 1*
+X:2699188_G_C X:2699188_G_C 2699188 G C 0 0 0 0 1 0 0 0 0 1 1 0 1 0 0 0 0 0 0 1
+X:2699189_T_C X:2699189_T_C 2699189 T C 0 0 0 0 1 0 0 0 0 1 1 0 1 0 0 0 0 0 0 1
+X:2699217_C_T X:2699217_C_T 2699217 C T 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+X:2699246_C_A X:2699246_C_A 2699246 C A 1 0 1 1 0 1 1 1 1 0 0 1 0 0 0 1 0 0 1 0
+X:2699275_T_G X:2699275_T_G 2699275 T G 0 0 0 0 1 0 0 0 0 1 1 1 1 0 0 0 0 0 0 1
+X:2699350_A_T X:2699350_A_T 2699350 A T 0 0 0 0 1 0 0 0 0 1 1 0 1 0 0 0 0 0 0 1
+X:2699360_T_C X:2699360_T_C 2699360 T C 0 0 0 0 1 0 0 0 0 1 1 0 1 0 0 0 0 0 0 1
+X:2699450_A_C X:2699450_A_C 2699450 A C 0 0 0 0 1 0 0 0 0 1 1 0 1 0 0 0 0 0 0 1
+X:2699507_T_C X:2699507_T_C 2699507 T C 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+X:2699555_C_A X:2699555_C_A 2699555 C A 0 - 1 - 1 - 0 - 1 - 1 1 1 0 0 1 0 0 0 1
+X:2699645_G_T X:2699645_G_T 2699645 G T 0 - 1 - 0 - 0 - 0 - 0 0 0 0 0 1 0 0 0 0
+X:2699676_G_A X:2699676_G_A 2699676 G A 0 - 0 - 1 - 0 - 1 - 1 0 1 0 0 0 0 0 0 1
+X:2699728_C_T X:2699728_C_T 2699728 C T 0 - 0 - 0 - 0 - 0 - 0 0 0 0 0 0 0 0 0 0
+X:2699775_C_A X:2699775_C_A 2699775 C A 0 - 0 - 0 - 0 - 0 - 0 0 0 0 0 0 0 0 0 0
+X:2699898_C_CT X:2699898_C_CT 2699898 C CT 0 - 0 - 1 - 0 - 1 - 1 0 1 0 0 0 0 0 0 1
+X:2699968_A_G X:2699968_A_G 2699968 A G ? - 0 - 0 - 1 - 0 - 0 1 0 0 0 0 0 1 1 0
+X:2699970_T_C X:2699970_T_C 2699970 T C 0 - 0 - 0 - 0 - 0 - 0 0 0 0 0 0 0 0 0 0
+X:2699990_C_<INS:ME:LINE1>_2700054 X:2699990_C_<INS:ME:LINE1>_2700054 2699990 C <INS:ME:LINE1> 0 0 0 0 1 0 0 0 0 1 1 0 1 0 0 0 0 0 0 1
diff --git a/test/convert.hs.gt.samples b/test/convert.hs.gt.samples
new file mode 100644
index 0000000..080f72a
--- /dev/null
+++ b/test/convert.hs.gt.samples
@@ -0,0 +1,12 @@
+ID_1 ID_2 missing
+0 0 0
+NA00001 NA00001 0
+NA00002 NA00002 0
+NA00003 NA00003 0
+NA00004 NA00004 0
+NA00005 NA00005 0
+NA00006 NA00006 0
+NA00007 NA00007 0
+NA00008 NA00008 0
+NA00009 NA00009 0
+NA00010 NA00010 0
diff --git a/test/fill-tags.out b/test/fill-tags.out
new file mode 100644
index 0000000..eb8676f
--- /dev/null
+++ b/test/fill-tags.out
@@ -0,0 +1,40 @@
+##fileformat=VCFv4.1
+##FILTER=<ID=PASS,Description="All filters passed">
+##INFO=<ID=TEST,Number=1,Type=Integer,Description="Testing Tag">
+##FORMAT=<ID=TT,Number=A,Type=Integer,Description="Testing Tag, with commas and \"escapes\" and escaped escapes combined with \\\"quotes\\\\\"">
+##INFO=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
+##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood">
+##FILTER=<ID=q10,Description="Quality below 10">
+##FILTER=<ID=test,Description="Testing filter">
+##contig=<ID=1,assembly=b37,length=249250621>
+##contig=<ID=2,assembly=b37,length=249250621>
+##contig=<ID=3,assembly=b37,length=198022430>
+##contig=<ID=4,assembly=b37,length=191154276>
+##reference=file:///lustre/scratch105/projects/g1k/ref/main_project/human_g1k_v37.fasta
+##readme=AAAAAA
+##readme=BBBBBB
+##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
+##INFO=<ID=STR,Number=1,Type=String,Description="Test string type">
+##INFO=<ID=AC_Hom,Number=A,Type=Integer,Description="Allele counts in homozygous genotypes">
+##INFO=<ID=AC_Het,Number=A,Type=Integer,Description="Allele counts in heterozygous genotypes">
+##INFO=<ID=AC_Hemi,Number=A,Type=Integer,Description="Allele counts in hemizygous genotypes">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	A	B
+1	3000150	.	C	T	59.2	PASS	AN=4;AC=2;AC_Het=2;AC_Hom=0;AC_Hemi=0	GT:GQ	0/1:245	0/1:245
+1	3000151	.	C	T	59.2	PASS	AN=4;AC=2;AC_Het=2;AC_Hom=0;AC_Hemi=0	GT:DP:GQ	0/1:32:245	0/1:32:245
+1	3062915	id3D	GTTT	G	12.9	q10	DP4=1,2,3,4;AN=4;AC=2;INDEL;STR=test;AC_Het=2;AC_Hom=0;AC_Hemi=0	GT:GQ:DP:GL	0/1:409:35:-20,-5,-20	0/1:409:35:-20,-5,-20
+1	3062915	idSNP	G	T,C	12.6	test	TEST=5;DP4=1,2,3,4;AN=3;AC=1,1;AC_Het=1,0;AC_Hom=0,0;AC_Hemi=0,1	GT:TT:GQ:DP:GL	0/1:0,1:409:35:-20,-5,-20,-20,-5,-20	2:0,1:409:35:-20,-5,-20
+1	3106154	.	CAAA	C	342	PASS	AN=4;AC=2;AC_Het=2;AC_Hom=0;AC_Hemi=0	GT:GQ:DP	0/1:245:32	0/1:245:32
+1	3106154	.	C	CT	59.2	PASS	AN=4;AC=2;AC_Het=2;AC_Hom=0;AC_Hemi=0	GT:GQ:DP	0/1:245:32	0/1:245:32
+1	3157410	.	GA	G	90.6	q10	AN=4;AC=4;AC_Het=0;AC_Hom=4;AC_Hemi=0	GT:GQ:DP	1/1:21:21	1/1:21:21
+1	3162006	.	GAA	G	60.2	PASS	AN=4;AC=2;AC_Het=2;AC_Hom=0;AC_Hemi=0	GT:GQ:DP	0/1:212:22	0/1:212:22
+1	3177144	.	G	T	45	PASS	AN=4;AC=2;AC_Het=0;AC_Hom=2;AC_Hemi=0	GT:GQ:DP	0/0:150:30	1/1:150:30
+1	3177144	.	G	.	45	PASS	AN=4	GT:GQ:DP	0/0:150:30	0/0:150:30
+1	3184885	.	TAAAA	TA,T	61.5	PASS	AN=4;AC=2,2;AC_Het=2,2;AC_Hom=0,0;AC_Hemi=0,0	GT:GQ:DP	1/2:12:10	1/2:12:10
+2	3199812	.	G	GTT,GT	82.7	PASS	AN=4;AC=2,2;AC_Het=2,2;AC_Hom=0,0;AC_Hemi=0,0	GT:GQ:DP	1/2:322:26	1/2:322:26
+3	3212016	.	CTT	C,CT	79	PASS	AN=4;AC=2,2;AC_Het=2,2;AC_Hom=0,0;AC_Hemi=0,0	GT:GQ:DP	1/2:91:26	1/2:91:26
+4	3258448	.	TACACACAC	T	.	PASS	AN=4;AC=2;AC_Het=2;AC_Hom=0;AC_Hemi=0	GT:GQ:DP	0/1:325:31	0/1:325:31
diff --git a/test/filter.10.out b/test/filter.10.out
new file mode 100644
index 0000000..0574390
--- /dev/null
+++ b/test/filter.10.out
@@ -0,0 +1,11 @@
+##fileformat=VCFv4.1
+##FILTER=<ID=PASS,Description="All filters passed">
+##contig=<ID=chr1,length=135006516>
+##INFO=<ID=TEST1,Number=1,Type=Integer,Description="Test1">
+##INFO=<ID=TEST2,Number=1,Type=Float,Description="Test2">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=TEST3,Number=1,Type=Integer,Description="Test3">
+##FORMAT=<ID=TEST4,Number=1,Type=Float,Description="Test4">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	sample1	sample2
+chr1	1	.	A	T	100	PASS	TEST1=10;TEST2=10	GT:TEST3:TEST4	0/1:10:10	./.:30:30
+chr1	2	.	A	T	100	PASS	TEST1=50;TEST2=50	GT:TEST3:TEST4	0/1:20:20	./.:40:40
diff --git a/test/merge.2.b.vcf b/test/filter.11.out
similarity index 73%
copy from test/merge.2.b.vcf
copy to test/filter.11.out
index fab439f..8b58d63 100644
--- a/test/merge.2.b.vcf
+++ b/test/filter.11.out
@@ -1,4 +1,5 @@
 ##fileformat=VCFv4.1
+##FILTER=<ID=PASS,Description="All filters passed">
 ##INFO=<ID=TEST,Number=1,Type=Integer,Description="Testing Tag">
 ##FORMAT=<ID=TT,Number=A,Type=Integer,Description="Testing Tag, with commas and \"escapes\" and escaped escapes combined with \\\"quotes\\\\\"">
 ##INFO=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
@@ -20,11 +21,6 @@
 ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
 ##INFO=<ID=STR,Number=1,Type=String,Description="Test string type">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	A	B
-1	3000000	.	C	G	59.2	PASS	AN=4;AC=2	GT:GQ	0/1:245	0/1:245
-1	3000150	.	C	G	59.2	PASS	AN=4;AC=2	GT:GQ	0/1:245	0/1:245
-1	3000151	.	C	G	59.2	PASS	AN=4;AC=2	GT:DP:GQ	0/1:32:245	0/1:32:245
-1	3106154	.	C	CCC	342	PASS	AN=4;AC=2	GT:GQ:DP	0/1:245:32	0/1:245:32
-1	3106154	.	C	T	59.2	PASS	AN=4;AC=2	GT:GQ:DP	0/1:245:32	0/1:245:32
-1	3200000	.	C	T	59.2	PASS	AN=4;AC=2	GT:GQ:DP	0/1:245:32	0/1:245:32
-1	3200010	.	C	A,T	59.2	PASS	AN=4;AC=2	GT:GQ:DP	0/1:245:32	0/1:245:32
-1	3200020	.	C	T,G	59.2	PASS	AN=4;AC=2	GT:GL	./.:1,4,6,2,5,3	.:1,3,2
+1	3106154	.	CAAA	C	342	PASS	AN=4;AC=2	GT:GQ:DP	0/1:245:32	0/1:25:300
+1	3106154	.	C	CT	59.2	PASS	AN=4;AC=2	GT:GQ:DP	0/1:25:12	0/1:245:310
+1	3157410	.	GA	G	90.6	q10	AN=4;AC=4	GT:GQ:DP	1/1:21:21	1/1:21:21
diff --git a/test/filter.4.vcf b/test/filter.4.vcf
new file mode 100644
index 0000000..78ce13a
--- /dev/null
+++ b/test/filter.4.vcf
@@ -0,0 +1,10 @@
+##fileformat=VCFv4.1
+##contig=<ID=chr1,length=135006516>
+##INFO=<ID=TEST1,Number=1,Type=Integer,Description="Test1">
+##INFO=<ID=TEST2,Number=1,Type=Float,Description="Test2">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=TEST3,Number=1,Type=Integer,Description="Test3">
+##FORMAT=<ID=TEST4,Number=1,Type=Float,Description="Test4">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	sample1	sample2
+chr1	1	.	A	T	100	.	TEST1=10;TEST2=10	GT:TEST3:TEST4	0/1:10:10	0/1:30:30
+chr1	2	.	A	T	100	.	TEST1=50;TEST2=50	GT:TEST3:TEST4	0/1:20:20	0/1:40:40
diff --git a/test/filter.9.out b/test/filter.9.out
new file mode 100644
index 0000000..3bf2f5c
--- /dev/null
+++ b/test/filter.9.out
@@ -0,0 +1 @@
+3177144	0	0/0	0/0
diff --git a/test/gvcf.fa b/test/gvcf.fa
new file mode 100644
index 0000000..45c4d5b
--- /dev/null
+++ b/test/gvcf.fa
@@ -0,0 +1,9 @@
+>22
+NNNNNNNNCCTTGGCCAAGTCACTTCCTCCTTCAGGAACATTGCAGTGGGCCTAAGTGCC
+TCCTCTCGGGACTGGTATGGGGACGGTCATGCAATCTGGACAACATTCACCTTTAAAAGT
+TTATTGATCTTTTGTGACATGCACGTGGGTTCCCAGTAGCAAGAAACTAAAGGGTCGCAG
+GCCGGTTTCTGCTAATTTCTTTAATTCCAAGACAGTCTCAAATATTTTCTTATTAACTTC
+CTGGAGGGAGGCTTATCATTCTCTCTTTTGGATGATTCTAAGTACCAGCTAAAATACAGC
+TATCATTCATTTTCCTTGATTTGGGAGCCTAATTTCTTTAATTTAGTATGCAAGAAAACC
+AATTTGGAAATATCAACTGTTTTGGAAACCTTAGACCTAGGTCATCCTTAGTAAGATCTT
+CCCATTTATATAAATACTTGCAAGTAGTAGTGCCATAATT
diff --git a/test/gvcf.fa.fai b/test/gvcf.fa.fai
new file mode 100644
index 0000000..4f07c21
--- /dev/null
+++ b/test/gvcf.fa.fai
@@ -0,0 +1 @@
+22	460	4	60	61
diff --git a/test/many.alleles.trim.out b/test/many.alleles.trim.out
new file mode 100644
index 0000000..7b622e1
--- /dev/null
+++ b/test/many.alleles.trim.out
@@ -0,0 +1,10 @@
+##fileformat=VCFv4.1
+##FILTER=<ID=PASS,Description="All filters passed">
+##contig=<ID=chr7>
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	SRR1528791
+chr7	142459798	.	CCATCTCTCTGCCCA	CCATCTCTCTCCCCG	.	.	AC=2;AN=2	GT	1/1
+chr7	142459798	.	CCATCTCTCTGCCCA	CCATCTCTCTCCCCG	.	.	AC=2;AN=2	GT	1/1
+chr7	142459798	.	CCATCTCTCTGCCCA	CCATCTCTCTCCCCG	.	.	AC=2;AN=2	GT	1/1
diff --git a/test/many.alleles.vcf b/test/many.alleles.vcf
new file mode 100644
index 0000000..491bc89
--- /dev/null
+++ b/test/many.alleles.vcf
@@ -0,0 +1,7 @@
+##fileformat=VCFv4.1
+##contig=<ID=chr7>
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	SRR1528791
+chr7	142459798	.	CCATCTCTCTGCCCA	CCATCTCTCTCCCCC,CCATCTCTCTCCCCG,CCTTCTCTCTGCCCC,CCCTCTCTCTCCCCC,CCACCTCTCTGCCCC,CCACCCCTCTGCCCA,CCACCTCCCTCCCCC,CCACCTCCCTGCCCA,CCACCTCTCGGCCCC,CCACCTCTCGGCCCA,CCACCTCTCTCCCCC,CCACCTCTCTCCCCA,CCATCCCCCTCCCCC,CCATCCCCCTGCCCC,CCATCCCCCTGCCCA,CCATCCCTCGGCCCC,CCATCCCTCGGCCCA,CCATCCCTCTCCCCC,CCATCCCTCTCCCCA,CCATCCCTCTGCCCC,CCATCTCCCGGCCCC,CCATCTCCCGGCCCA,CCATCTCCCGCCCCC,CCATCTCCCTCCCCC,CCATCTCCCTCCCCA,CCATCTCCCTGCCCC,CCATCTCTCGGCCCC,CCATCTCTCCCCCCC,CCATCTCTCGC [...]
+chr7	142459798	.	CCATCTCTCTGCCCA	CCATCTCTCTCCCCC,CCATCTCTCTCCCCG,CCTTCTCTCTGCCCC,CCCTCTCTCTCCCCC,CCACCTCTCTGCCCC,CCACCCCTCTGCCCA,CCACCTCCCTCCCCC,CCACCTCCCTGCCCA,CCACCTCTCGGCCCC,CCACCTCTCGGCCCA,CCACCTCTCTCCCCC,CCACCTCTCTCCCCA,CCATCCCCCTCCCCC,CCATCCCCCTGCCCC,CCATCCCCCTGCCCA,CCATCCCTCGGCCCC,CCATCCCTCGGCCCA,CCATCCCTCTCCCCC,CCATCCCTCTCCCCA,CCATCCCTCTGCCCC,CCATCTCCCGGCCCC,CCATCTCCCGGCCCA,CCATCTCCCGCCCCC,CCATCTCCCTCCCCC,CCATCTCCCTCCCCA,CCATCTCCCTGCCCC,CCATCTCTCGGCCCC,CCATCTCTCCCCCCC,CCATCTCTCGC [...]
+chr7	142459798	.	CCATCTCTCTGCCCA	CCATCTCTCTCCCCC,CCATCTCTCTCCCCG,CCTTCTCTCTGCCCC,CCCTCTCTCTCCCCC,CCACCTCTCTGCCCC,CCACCCCTCTGCCCA,CCACCTCCCTCCCCC,CCACCTCTCGGCCCC,CCACCTCTCGGCCCA,CCACCTCTCTCCCCC,CCACCTCTCTCCCCA,CCATCCCCCTCCCCC,CCATCCCCCTGCCCC,CCATCCCCCTGCCCA,CCATCCCTCGGCCCC,CCATCCCTCGGCCCA,CCATCCCTCTCCCCC,CCATCCCTCTCCCCA,CCATCCCTCTGCCCC,CCATCTCCCGGCCCC,CCATCTCCCGGCCCA,CCATCTCCCGCCCCC,CCATCTCCCTCCCCC,CCATCTCCCTCCCCA,CCATCTCCCTGCCCC,CCATCTCTCGGCCCC,CCATCTCTCCCCCCC,CCATCTCTCGCCCCC,CCATCTCTGGG [...]
diff --git a/test/merge.2.b.vcf b/test/merge.2.b.vcf
index fab439f..8700f1c 100644
--- a/test/merge.2.b.vcf
+++ b/test/merge.2.b.vcf
@@ -26,5 +26,5 @@
 1	3106154	.	C	CCC	342	PASS	AN=4;AC=2	GT:GQ:DP	0/1:245:32	0/1:245:32
 1	3106154	.	C	T	59.2	PASS	AN=4;AC=2	GT:GQ:DP	0/1:245:32	0/1:245:32
 1	3200000	.	C	T	59.2	PASS	AN=4;AC=2	GT:GQ:DP	0/1:245:32	0/1:245:32
-1	3200010	.	C	A,T	59.2	PASS	AN=4;AC=2	GT:GQ:DP	0/1:245:32	0/1:245:32
+1	3200010	.	c	A,T	59.2	PASS	AN=4;AC=2	GT:GQ:DP	0/1:245:32	0/1:245:32
 1	3200020	.	C	T,G	59.2	PASS	AN=4;AC=2	GT:GL	./.:1,4,6,2,5,3	.:1,3,2
diff --git a/test/annotate5.out b/test/missing.vcf
similarity index 59%
copy from test/annotate5.out
copy to test/missing.vcf
index d3ab764..b6ca53d 100644
--- a/test/annotate5.out
+++ b/test/missing.vcf
@@ -1,5 +1,4 @@
 ##fileformat=VCFv4.1
-##FILTER=<ID=PASS,Description="All filters passed">
 ##contig=<ID=1,assembly=b37,length=249250621>
 ##reference=file:///lustre/scratch105/projects/g1k/ref/main_project/human_g1k_v37.fasta
 ##INFO=<ID=FLAG,Number=0,Type=Flag,Description="Test type">
@@ -11,9 +10,9 @@
 ##FORMAT=<ID=FFLT,Number=1,Type=Float,Description="Test type">
 ##FORMAT=<ID=FSTR,Number=1,Type=String,Description="Test type">
 ##FILTER=<ID=q11,Description="Quality below 10">
-##FILTER=<ID=q99,Description="Quality below 10">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	A	B	C
-1	3000001	xx	C	T	11	PASS	IINT=11;IFLT=1.1;ISTR=xxx	GT:FINT:FFLT:FSTR	.:11:1.1:xxx	0/0:11:1.1:x	0/0:11:1.1:x
-1	3000002	id	C	T	99	q99	FLAG;IINT=88,99;IFLT=8.8,9.9;ISTR=888,999	GT	0|1	.	.
-1	3000003	id	C	T	99	q11;q99	FLAG;IINT=88,99;IFLT=8.8,9.9;ISTR=888,999	GT:FINT:FFLT:FSTR	0|1:.:.:.	0/0:.:.:.	0/0:.:.:.
-1	3000004	id	C	T	99	q11;q99	FLAG;IINT=11;IFLT=1.1;ISTR=xxx	GT:FINT:FFLT:FSTR	0|1:11:1.1:x	0/0:11:1.1:xxx	0/0:11:1.1:xxx
+1	3000001	xx	C	T	11	PASS	FLAG;IINT=11;IFLT=1.1;ISTR=xxx	GT:FINT:FFLT:FSTR	0/0:11:1.1:xxx	0/0:11:1.1:x	0/0:11:1.1:x
+1	3000002	.	C	T	.	.	.	GT	.	.	.
+1	3000003	xx	C	T	11	q11	FLAG;IINT=.;IFLT=.;ISTR=.	GT:FINT:FFLT:FSTR	0/0:.:.:.	0/0:.:.:.	0/0:.:.:.
+1	3000004	xx	C	T	11	q11	FLAG;IINT=11;IFLT=1.1;ISTR=xxx	GT:FINT:FFLT:FSTR	0/0:11:1.1:x	0/0:11:1.1:xxx	0/0:11:1.1:xxx
+1	3000005	xx	C	T	11	q11	FLAG;IINT=1;IFLT=1;ISTR=..	GT:FINT:FFLT:FSTR	0/0:11:1.1:x	0/0:11:1.1:xxx	0/0:11:1.1:xxx
diff --git a/test/mpileup.2.out b/test/mpileup.2.out
index 4a415ea..d657160 100644
--- a/test/mpileup.2.out
+++ b/test/mpileup.2.out
@@ -19,6 +19,8 @@
 ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">
 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Number of high-quality bases">
 ##FORMAT=<ID=DV,Number=1,Type=Integer,Description="Number of high-quality non-reference bases">
+##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
+##INFO=<ID=MinDP,Number=1,Type=Integer,Description="Minimum per-sample depth in this gVCF block">
 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
 ##INFO=<ID=ICB,Number=1,Type=Float,Description="Inbreeding Coefficient Binomial test (bigger is better)">
 ##INFO=<ID=HOB,Number=1,Type=Float,Description="Bias in the number of HOMs number (smaller is better)">
@@ -26,28 +28,27 @@
 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
 ##INFO=<ID=DP4,Number=4,Type=Integer,Description="Number of high-quality ref-forward , ref-reverse, alt-forward and alt-reverse bases">
 ##INFO=<ID=MQ,Number=1,Type=Integer,Description="Average mapping quality">
-##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	HG00100	HG00101	HG00102
-17	1	.	A	.	.	.	END=301	GT	0/0	0/0	0/0
+17	1	.	A	.	.	.	END=301;MinDP=1	GT:DP	./.:5	./.:1	./.:3
 17	302	.	T	TA	488	.	INDEL;IDV=7;IMF=1;DP=25;VDB=0.27613;SGB=-4.22417;MQSB=0.0443614;MQ0F=0;ICB=0.8;HOB=0.222222;AC=4;AN=6;DP4=2,4,8,11;MQ=49	GT:PL:DP:DV	0/1:167,0,96:11:6	0/1:157,0,9:7:6	1/1:201,21,0:7:7
-17	303	.	G	.	.	.	END=827	GT	0/0	0/0	0/0
+17	303	.	G	.	.	.	END=827;MinDP=2	GT:DP	0/0:9	0/0:2	0/0:3
 17	828	.	T	C	409	.	DP=25;VDB=0.842082;SGB=-4.20907;RPB=0.950652;MQB=1;MQSB=1;BQB=0.929717;MQ0F=0;ICB=0.8;HOB=0.222222;AC=4;AN=6;DP4=2,4,8,11;MQ=60	GT:PL:DP:DV	0/1:211,0,35:12:10	0/1:116,0,91:9:5	1/1:120,12,0:4:4
-17	829	.	T	.	.	.	END=833	GT	0/0	0/0	0/0
+17	829	.	T	.	.	.	END=833;MinDP=4	GT:DP	0/0:11	0/0:8	0/0:4
 17	834	.	G	A	364	.	DP=25;VDB=0.788006;SGB=-4.01214;RPB=0.999233;MQB=1;MQSB=1;BQB=0.821668;MQ0F=0;ICB=0.8;HOB=0.222222;AC=4;AN=6;DP4=2,3,7,10;MQ=60	GT:PL:DP:DV	0/1:185,0,46:11:9	0/1:128,0,59:8:5	1/1:89,9,0:3:3
-17	835	.	T	.	.	.	END=1664	GT	0/0	0/0	0/0
+17	835	.	T	.	.	.	END=1664;MinDP=1	GT:DP	0/0:5	0/0:2	0/0:1
 17	1665	.	T	C	3.10665	.	DP=20;VDB=0.1;SGB=0.346553;RPB=0.222222;MQB=0.611111;MQSB=0.988166;BQB=0.944444;MQ0F=0;ICB=0.128205;HOB=0.0555556;AC=1;AN=6;DP4=7,11,1,1;MQ=55	GT:PL:DP:DV	0/0:0,21,185:7:0	0/0:0,27,222:9:0	0/1:35,0,51:4:2
-17	1666	.	G	.	.	.	END=1868	GT	0/0	0/0	0/0
+17	1666	.	G	.	.	.	END=1868;MinDP=0	GT:DP	0/0:6	0/0:0	0/0:1
 17	1869	.	A	T	138	.	DP=24;VDB=0.928022;SGB=-11.9537;RPB=0.984127;MQB=0.96464;MQSB=0.931547;BQB=0.359155;MQ0F=0;ICB=0.8;HOB=0.222222;AC=4;AN=6;DP4=6,9,5,4;MQ=58	GT:PL:DP:DV	0/1:115,0,224:18:7	0/1:16,0,104:5:1	1/1:42,3,0:1:1
-17	1870	.	C	.	.	.	END=2040	GT	0/0	0/0	0/0
+17	1870	.	C	.	.	.	END=2040;MinDP=1	GT:DP	0/0:13	0/0:2	0/0:1
 17	2041	.	G	A	447	.	DP=31;VDB=0.816435;SGB=-4.18892;RPB=0.88473;MQB=0.972375;MQSB=0.968257;BQB=0.311275;MQ0F=0;ICB=0.8;HOB=0.222222;AC=4;AN=6;DP4=6,5,12,7;MQ=58	GT:PL:DP:DV	0/1:229,0,212:21:11	0/1:32,0,24:2:1	1/1:223,21,0:7:7
-17	2042	.	G	.	.	.	END=2219	GT	0/0	0/0	0/0
+17	2042	.	G	.	.	.	END=2219;MinDP=1	GT:DP	0/0:8	0/0:1	0/0:3
 17	2220	.	G	A	303	.	DP=21;VDB=0.532753;SGB=-3.51597;RPB=0.964198;MQB=0.898397;MQSB=0.875769;BQB=0.0354359;MQ0F=0;ICB=0.8;HOB=0.222222;AC=4;AN=6;DP4=6,2,1,11;MQ=58	GT:PL:DP:DV	0/1:139,0,130:12:6	0/1:69,0,46:4:2	1/1:131,12,0:4:4
-17	2221	.	G	.	.	.	END=2563	GT	0/0	0/0	0/0
+17	2221	.	G	.	.	.	END=2563;MinDP=0	GT:DP	0/0:5	0/0:0	0/0:2
 17	2564	.	A	G	233	.	DP=15;VDB=0.690812;SGB=-3.20711;RPB=0.197899;MQB=1;MQSB=1;BQB=0.965069;MQ0F=0;ICB=0.8;HOB=0.222222;AC=4;AN=6;DP4=1,4,4,5;MQ=60	GT:PL:DP:DV	0/1:88,0,78:6:3	0/1:57,0,56:4:2	1/1:124,12,0:4:4
-17	2565	.	A	.	.	.	END=3103	GT	0/0	0/0	0/0
+17	2565	.	A	.	.	.	END=3103;MinDP=0	GT:DP	0/0:6	0/0:0	0/0:1
 17	3104	.	C	T	24.2837	.	DP=25;VDB=0.8;SGB=0.346553;RPB=0.717391;MQB=0.956522;MQSB=0.962269;BQB=0.978261;MQ0F=0;ICB=0.128205;HOB=0.0555556;AC=1;AN=6;DP4=8,15,2,0;MQ=58	GT:PL:DP:DV	0/0:0,48,255:16:0	0/0:0,12,144:4:0	0/1:59,0,93:5:2
-17	3105	.	T	.	.	.	END=3586	GT	0/0	0/0	0/0
+17	3105	.	T	.	.	.	END=3586;MinDP=2	GT:DP	0/0:5	0/0:2	0/0:3
 17	3587	.	G	A	358	.	DP=29;VDB=0.902044;SGB=-3.91326;RPB=0.800999;MQB=1;MQSB=1;BQB=0.156944;MQ0F=0;ICB=0.8;HOB=0.222222;AC=4;AN=6;DP4=4,7,10,6;MQ=60	GT:PL:DP:DV	0/1:161,0,184:14:7	0/1:22,0,118:5:1	1/1:212,24,0:8:8
-17	3588	.	A	.	.	.	END=3935	GT	0/0	0/0	0/0
+17	3588	.	A	.	.	.	END=3935;MinDP=2	GT:DP	0/0:10	0/0:2	0/0:3
 17	3936	.	A	G	469	.	DP=37;VDB=0.0574114;SGB=-4.60123;RPB=0.741697;MQB=0.812605;MQSB=0.143788;BQB=0.883831;MQ0F=0;ICB=0.8;HOB=0.222222;AC=4;AN=6;DP4=5,6,6,17;MQ=56	GT:PL:DP:DV	0/1:233,0,206:20:11	0/1:77,0,58:6:4	1/1:196,24,0:8:8
-17	3937	.	C	.	.	.	END=4101	GT	0/0	0/0	0/0
+17	3937	.	C	.	.	.	END=4101;MinDP=0	GT:DP	0/0:1	0/0:0	0/0:0
diff --git a/test/mpileup.cAls.out b/test/mpileup.X.out
similarity index 51%
copy from test/mpileup.cAls.out
copy to test/mpileup.X.out
index 660e7f5..9a9d427 100644
--- a/test/mpileup.cAls.out
+++ b/test/mpileup.X.out
@@ -3,7 +3,7 @@
 ##samtoolsVersion=1.1-19-g6b249e2+htslib-1.1-74-g845c515
 ##samtoolsCommand=samtools mpileup -uvDV -b xxx//mpileup.bam.list -f xxx//mpileup.ref.fa.gz
 ##reference=file://xxx//mpileup.ref.fa.gz
-##contig=<ID=17,length=81195210>
+##contig=<ID=X,length=81195210>
 ##ALT=<ID=X,Description="Represents allele(s) other than observed.">
 ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
 ##INFO=<ID=IDV,Number=1,Type=Integer,Description="Maximum number of reads supporting an indel">
@@ -27,7 +27,14 @@
 ##INFO=<ID=DP4,Number=4,Type=Integer,Description="Number of high-quality ref-forward , ref-reverse, alt-forward and alt-reverse bases">
 ##INFO=<ID=MQ,Number=1,Type=Integer,Description="Average mapping quality">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	HG00100	HG00101	HG00102
-17	828	.	T	C	409	.	DP=25;VDB=0.842082;SGB=-4.20907;RPB=0.950652;MQB=1;MQSB=1;BQB=0.929717;MQ0F=0;ICB=0.8;HOB=0.222222;AC=4;AN=6;DP4=2,4,8,11;MQ=60	GT:PL:DP:DV	0/1:211,0,35:12:10	0/1:116,0,91:9:5	1/1:120,12,0:4:4
-17	1665	.	T	C	3.10665	.	DP=20;VDB=0.1;SGB=0.346553;RPB=0.222222;MQB=0.611111;MQSB=0.988166;BQB=0.944444;MQ0F=0;ICB=0.128205;HOB=0.0555556;AC=1;AN=6;DP4=7,11,1,1;MQ=55	GT:PL:DP:DV	0/0:0,21,185:7:0	0/0:0,27,222:9:0	0/1:35,0,51:4:2
-17	2220	.	G	C	999	.	DP=21;VDB=0.532753;SGB=-3.51597;RPB=0.964198;MQB=0.898397;MQSB=0.875769;BQB=0.0354359;MQ0F=0;AC=0;AN=6;DP4=6,2,1,11;MQ=58	GT:PL:DP:DV	0/0:139,157,255:12:6	0/0:69,75,119:4:2	0/0:131,131,131:4:4
-17	2564	.	A	AG	999	.	DP=15;VDB=0.690812;SGB=-3.20711;RPB=0.197899;MQB=1;MQSB=1;BQB=0.965069;MQ0F=0;AC=0;AN=6;DP4=1,4,4,5;MQ=60	GT:PL:DP:DV	0/0:88,98,171:6:3	0/0:57,63,117:4:2	0/0:124,124,124:4:4
+X	302	.	T	TA	481	.	INDEL;IDV=7;IMF=1;DP=25;VDB=0.27613;SGB=-4.22417;MQSB=0.0443614;MQ0F=0;ICB=0.235294;HOB=0.18;AC=4;AN=5;DP4=2,4,8,11;MQ=49	GT:PL:DP:DV	0/1:167,0,96:11:6	1:157,9:7:6	1/1:201,21,0:7:7
+X	828	.	T	C	321	.	DP=25;VDB=0.842082;SGB=-4.20907;RPB=0.950652;MQB=1;MQSB=1;BQB=0.929717;MQ0F=0;ICB=0.235294;HOB=0.18;AC=4;AN=5;DP4=2,4,8,11;MQ=60	GT:PL:DP:DV	0/1:211,0,35:12:10	1:116,91:9:5	1/1:120,12,0:4:4
+X	834	.	G	A	308	.	DP=25;VDB=0.788006;SGB=-4.01214;RPB=0.999233;MQB=1;MQSB=1;BQB=0.821668;MQ0F=0;ICB=0.235294;HOB=0.18;AC=4;AN=5;DP4=2,3,7,10;MQ=60	GT:PL:DP:DV	0/1:185,0,46:11:9	1:128,59:8:5	1/1:89,9,0:3:3
+X	1665	.	T	C	3.10665	.	DP=20;VDB=0.1;SGB=0.346553;RPB=0.222222;MQB=0.611111;MQSB=0.988166;BQB=0.944444;MQ0F=0;ICB=0.128205;HOB=0.0555556;AC=1;AN=6;DP4=7,11,1,1;MQ=55	GT:PL:DP:DV	0/0:0,21,185:7:0	0/0:0,27,222:9:0	0/1:35,0,51:4:2
+X	1869	.	A	T	138	.	DP=24;VDB=0.928022;SGB=-11.9537;RPB=0.984127;MQB=0.96464;MQSB=0.931547;BQB=0.359155;MQ0F=0;ICB=0.8;HOB=0.222222;AC=4;AN=6;DP4=6,9,5,4;MQ=58	GT:PL:DP:DV	0/1:115,0,224:18:7	0/1:16,0,104:5:1	1/1:42,3,0:1:1
+X	2041	.	G	A	447	.	DP=31;VDB=0.816435;SGB=-4.18892;RPB=0.88473;MQB=0.972375;MQSB=0.968257;BQB=0.311275;MQ0F=0;ICB=0.8;HOB=0.222222;AC=4;AN=6;DP4=6,5,12,7;MQ=58	GT:PL:DP:DV	0/1:229,0,212:21:11	0/1:32,0,24:2:1	1/1:223,21,0:7:7
+X	2220	.	G	A	303	.	DP=21;VDB=0.532753;SGB=-3.51597;RPB=0.964198;MQB=0.898397;MQSB=0.875769;BQB=0.0354359;MQ0F=0;ICB=0.8;HOB=0.222222;AC=4;AN=6;DP4=6,2,1,11;MQ=58	GT:PL:DP:DV	0/1:139,0,130:12:6	0/1:69,0,46:4:2	1/1:131,12,0:4:4
+X	2564	.	A	G	233	.	DP=15;VDB=0.690812;SGB=-3.20711;RPB=0.197899;MQB=1;MQSB=1;BQB=0.965069;MQ0F=0;ICB=0.8;HOB=0.222222;AC=4;AN=6;DP4=1,4,4,5;MQ=60	GT:PL:DP:DV	0/1:88,0,78:6:3	0/1:57,0,56:4:2	1/1:124,12,0:4:4
+X	3104	.	C	T	24.1975	.	DP=25;VDB=0.8;SGB=0.346553;RPB=0.717391;MQB=0.956522;MQSB=0.962269;BQB=0.978261;MQ0F=0;ICB=0.235294;HOB=0.18;AC=1;AN=5;DP4=8,15,2,0;MQ=58	GT:PL:DP:DV	0/0:0,48,255:16:0	0:0,144:4:0	0/1:59,0,93:5:2
+X	3587	.	G	A	332	.	DP=29;VDB=0.902044;SGB=-3.91326;RPB=0.800999;MQB=1;MQSB=1;BQB=0.156944;MQ0F=0;ICB=0.461538;HOB=0.02;AC=3;AN=5;DP4=4,7,10,6;MQ=60	GT:PL:DP:DV	0/1:161,0,184:14:7	0:22,118:5:1	1/1:212,24,0:8:8
+X	3936	.	A	G	412	.	DP=37;VDB=0.0574114;SGB=-4.60123;RPB=0.741697;MQB=0.812605;MQSB=0.143788;BQB=0.883831;MQ0F=0;ICB=0.235294;HOB=0.18;AC=4;AN=5;DP4=5,6,6,17;MQ=56	GT:PL:DP:DV	0/1:233,0,206:20:11	1:77,58:6:4	1/1:196,24,0:8:8
diff --git a/test/mpileup.X.vcf b/test/mpileup.X.vcf
new file mode 100644
index 0000000..ea2983a
--- /dev/null
+++ b/test/mpileup.X.vcf
@@ -0,0 +1,4127 @@
+##fileformat=VCFv4.2
+##FILTER=<ID=PASS,Description="All filters passed">
+##samtoolsVersion=1.1-19-g6b249e2+htslib-1.1-74-g845c515
+##samtoolsCommand=samtools mpileup -uvDV -b xxx//mpileup.bam.list -f xxx//mpileup.ref.fa.gz
+##reference=file://xxx//mpileup.ref.fa.gz
+##contig=<ID=X,length=81195210>
+##ALT=<ID=X,Description="Represents allele(s) other than observed.">
+##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
+##INFO=<ID=IDV,Number=1,Type=Integer,Description="Maximum number of reads supporting an indel">
+##INFO=<ID=IMF,Number=1,Type=Float,Description="Maximum fraction of reads supporting an indel">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">
+##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias for filtering splice-site artefacts in RNA-seq data (bigger is better)",Version="3">
+##INFO=<ID=RPB,Number=1,Type=Float,Description="Mann-Whitney U test of Read Position Bias (bigger is better)">
+##INFO=<ID=MQB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality Bias (bigger is better)">
+##INFO=<ID=BQB,Number=1,Type=Float,Description="Mann-Whitney U test of Base Quality Bias (bigger is better)">
+##INFO=<ID=MQSB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality vs Strand Bias (bigger is better)">
+##INFO=<ID=SGB,Number=1,Type=Float,Description="Segregation based metric.">
+##INFO=<ID=MQ0F,Number=1,Type=Float,Description="Fraction of MQ0 reads (smaller is better)">
+##INFO=<ID=I16,Number=16,Type=Float,Description="Auxiliary tag used for calling, see description of bcf_callret1_t in bam2bcf.h">
+##INFO=<ID=QS,Number=R,Type=Float,Description="Auxiliary tag used for calling">
+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Number of high-quality bases">
+##FORMAT=<ID=DV,Number=1,Type=Integer,Description="Number of high-quality non-reference bases">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	HG00100	HG00101	HG00102
+X	1	.	A	<*>	0	.	DP=11;I16=11,0,0,0,452,18594,0,0,319,9251,0,0,223,4959,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,72:3:0
+X	2	.	A	<*>	0	.	DP=11;I16=11,0,0,0,439,17587,0,0,319,9251,0,0,226,5030,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,72:3:0
+X	3	.	G	<*>	0	.	DP=11;I16=11,0,0,0,431,16971,0,0,319,9251,0,0,229,5111,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,72:3:0
+X	4	.	C	<*>	0	.	DP=11;I16=11,0,0,0,423,16417,0,0,319,9251,0,0,232,5202,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,71:3:0
+X	5	.	T	<*>	0	.	DP=11;I16=11,0,0,0,450,18520,0,0,319,9251,0,0,234,5252,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,72:3:0
+X	6	.	T	<*>	0	.	DP=11;I16=11,0,0,0,403,14847,0,0,319,9251,0,0,236,5310,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,72:3:0
+X	7	.	C	<*>	0	.	DP=11;I16=11,0,0,0,446,18114,0,0,319,9251,0,0,237,5327,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,72:3:0
+X	8	.	T	<*>	0	.	DP=11;I16=11,0,0,0,465,19677,0,0,319,9251,0,0,238,5354,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,72:3:0
+X	9	.	C	<*>	0	.	DP=11;I16=11,0,0,0,447,18205,0,0,319,9251,0,0,239,5391,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,72:3:0
+X	10	.	A	<*>	0	.	DP=11;I16=11,0,0,0,426,16756,0,0,319,9251,0,0,240,5438,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,69:3:0
+X	11	.	C	<*>	0	.	DP=11;I16=11,0,0,0,413,15603,0,0,319,9251,0,0,241,5495,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,72:3:0
+X	12	.	C	<*>	0	.	DP=11;I16=11,0,0,0,438,17506,0,0,319,9251,0,0,242,5562,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,72:3:0
+X	13	.	C	<*>	0	.	DP=11;I16=11,0,0,0,437,17463,0,0,319,9251,0,0,243,5639,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,72:3:0
+X	14	.	T	<*>	0	.	DP=11;I16=11,0,0,0,453,18715,0,0,319,9251,0,0,242,5628,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,72:3:0
+X	15	.	G	<*>	0	.	DP=11;I16=11,0,0,0,439,17599,0,0,319,9251,0,0,240,5580,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,72:3:0
+X	16	.	T	<*>	0	.	DP=11;I16=11,0,0,0,426,16546,0,0,319,9251,0,0,238,5544,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,72:3:0
+X	17	.	T	<*>	0	.	DP=11;I16=11,0,0,0,407,15195,0,0,319,9251,0,0,235,5469,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,72:3:0
+X	18	.	C	<*>	0	.	DP=12;I16=12,0,0,0,450,17136,0,0,379,12851,0,0,231,5353,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,18,113:6:0	0,9,72:3:0	0,9,72:3:0
+X	19	.	C	<*>	0	.	DP=13;I16=13,0,0,0,502,19652,0,0,439,16451,0,0,228,5246,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,18,112:6:0	0,12,89:4:0	0,9,72:3:0
+X	20	.	T	<*>	0	.	DP=13;I16=13,0,0,0,532,21878,0,0,439,16451,0,0,226,5150,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,18,116:6:0	0,12,98:4:0	0,9,72:3:0
+X	21	.	G	<*>	0	.	DP=13;I16=13,0,0,0,498,19254,0,0,439,16451,0,0,224,5066,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,18,117:6:0	0,12,94:4:0	0,9,72:3:0
+X	22	.	C	<*>	0	.	DP=13;I16=13,0,0,0,511,20289,0,0,470,19210,0,0,223,4993,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,18,115:6:0	0,12,91:4:0	0,9,76:3:0
+X	23	.	A	<*>	0	.	DP=14;I16=14,0,0,0,513,19399,0,0,530,22810,0,0,223,4931,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,21,133:7:0	0,12,82:4:0	0,9,82:3:0
+X	24	.	T	<*>	0	.	DP=14;I16=14,0,0,0,534,20540,0,0,530,22810,0,0,224,4882,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,21,131:7:0	0,12,96:4:0	0,9,80:3:0
+X	25	.	A	<*>	0	.	DP=15;I16=15,0,0,0,561,21133,0,0,590,26410,0,0,225,4847,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,24,140:8:0	0,12,96:4:0	0,9,81:3:0
+X	26	.	G	<*>	0	.	DP=15;I16=15,0,0,0,591,23429,0,0,590,26410,0,0,227,4827,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,24,151:8:0	0,12,96:4:0	0,9,81:3:0
+X	27	.	A	<*>	0	.	DP=15;I16=15,0,0,0,588,23120,0,0,590,26410,0,0,229,4823,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,24,146:8:0	0,12,98:4:0	0,9,83:3:0
+X	28	.	T	<*>	0	.	DP=16;I16=16,0,0,0,605,23001,0,0,650,30010,0,0,231,4835,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,24,147:8:0	0,12,97:4:0	0,12,101:4:0
+X	29	.	A	<*>	0	.	DP=17;I16=17,0,0,0,615,22533,0,0,710,33610,0,0,234,4864,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,24,146:8:0	0,15,102:5:0	0,12,104:4:0
+X	30	.	A	<*>	0	.	DP=17;I16=17,0,0,0,660,25914,0,0,710,33610,0,0,238,4912,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,24,149:8:0	0,15,115:5:0	0,12,108:4:0
+X	31	.	T	<*>	0	.	DP=17;I16=17,0,0,0,656,25392,0,0,710,33610,0,0,242,4980,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,24,150:8:0	0,15,113:5:0	0,12,105:4:0
+X	32	.	T	<*>	0	.	DP=17;I16=17,0,0,0,605,21789,0,0,741,36369,0,0,247,5067,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,24,143:8:0	0,15,104:5:0	0,12,104:4:0
+X	33	.	G	<*>	0	.	DP=17;I16=17,0,0,0,659,25757,0,0,741,36369,0,0,252,5124,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,24,158:8:0	0,15,118:5:0	0,12,105:4:0
+X	34	.	C	<*>	0	.	DP=17;I16=17,0,0,0,658,25704,0,0,741,36369,0,0,257,5203,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,24,151:8:0	0,15,121:5:0	0,12,106:4:0
+X	35	.	A	<*>	0	.	DP=18;I16=18,0,0,0,677,25881,0,0,801,39969,0,0,262,5304,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,24,152:8:0	0,15,109:5:0	0,15,121:5:0
+X	36	.	T	<*>	0	.	DP=18;I16=18,0,0,0,678,25796,0,0,801,39969,0,0,268,5428,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,24,151:8:0	0,15,114:5:0	0,15,125:5:0
+X	37	.	G	<*>	0	.	DP=18;I16=18,0,0,0,685,26291,0,0,801,39969,0,0,274,5576,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,24,157:8:0	0,15,116:5:0	0,15,126:5:0
+X	38	.	A	<*>	0	.	DP=18;I16=18,0,0,0,697,27245,0,0,801,39969,0,0,280,5748,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,24,152:8:0	0,15,116:5:0	0,15,129:5:0
+X	39	.	C	<*>	0	.	DP=16;I16=16,0,0,0,591,22311,0,0,743,38287,0,0,288,5942,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,21,148:7:0	0,12,94:4:0	0,15,123:5:0
+X	40	.	A	<*>	0	.	DP=16;I16=16,0,0,0,630,24896,0,0,743,38287,0,0,295,6107,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,21,146:7:0	0,12,104:4:0	0,15,127:5:0
+X	41	.	A	<*>	0	.	DP=17;I16=17,0,0,0,645,24685,0,0,803,41887,0,0,302,6294,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,24,151:8:0	0,12,104:4:0	0,15,131:5:0
+X	42	.	T	<*>	0	.	DP=17;I16=17,0,0,0,618,23118,0,0,803,41887,0,0,310,6504,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,24,155:8:0	0,12,82:4:0	0,15,127:5:0
+X	43	.	T	<*>	0	.	DP=17;I16=17,0,0,0,631,23689,0,0,803,41887,0,0,318,6738,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,24,151:8:0	0,12,101:4:0	0,15,129:5:0
+X	44	.	G	<*>	0	.	DP=17;I16=17,0,0,0,664,26162,0,0,803,41887,0,0,324,6896,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,24,164:8:0	0,12,100:4:0	0,15,129:5:0
+X	45	.	C	<*>	0	.	DP=17;I16=17,0,0,0,657,25525,0,0,803,41887,0,0,329,7027,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,24,163:8:0	0,12,108:4:0	0,15,125:5:0
+X	46	.	C	<*>	0	.	DP=17;I16=17,0,0,0,646,25244,0,0,803,41887,0,0,334,7180,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,24,161:8:0	0,12,98:4:0	0,15,131:5:0
+X	47	.	T	<*>	0	.	DP=17;I16=17,0,0,0,700,28998,0,0,803,41887,0,0,339,7355,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,24,165:8:0	0,12,110:4:0	0,15,136:5:0
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+X	1111	.	T	<*>	0	.	DP=29;I16=22,6,0,0,1025,37919,0,0,1680,100800,0,0,552,12470,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,30,227:10:0	0,24,227:8:0	0,30,211:10:0
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+X	1118	.	T	<*>	0	.	DP=29;I16=24,4,0,0,1100,44802,0,0,1680,100800,0,0,539,12131,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,30,230:10:0	0,21,188:7:0	0,33,248:11:0
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+X	1926	.	T	<*>	0	.	DP=27;I16=14,13,0,0,1031,40057,0,0,1546,91130,0,0,545,12581,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,21,197:7:0	0,12,141:4:0
+X	1927	.	T	<*>	0	.	DP=27;I16=13,13,0,0,959,35773,0,0,1529,90841,0,0,538,12522,0,0;QS=3,0;MQSB=0.945959;MQ0F=0	PL:DP:DV	0,45,255:15:0	0,21,191:7:0	0,12,133:4:0
+X	1928	.	C	<*>	0	.	DP=27;I16=13,13,0,0,986,38264,0,0,1529,90841,0,0,538,12532,0,0;QS=3,0;MQSB=0.945959;MQ0F=0	PL:DP:DV	0,45,255:15:0	0,21,189:7:0	0,12,125:4:0
+X	1929	.	T	<*>	0	.	DP=27;I16=13,13,0,0,990,38630,0,0,1529,90841,0,0,538,12562,0,0;QS=3,0;MQSB=0.945959;MQ0F=0	PL:DP:DV	0,45,255:15:0	0,21,189:7:0	0,12,139:4:0
+X	1930	.	G	<*>	0	.	DP=26;I16=13,11,0,0,905,34865,0,0,1409,83641,0,0,521,12271,0,0;QS=3,0;MQSB=0.931547;MQ0F=0	PL:DP:DV	0,45,255:15:0	0,18,179:6:0	0,9,99:3:0
+X	1931	.	C	<*>	0	.	DP=27;I16=15,12,0,0,967,36293,0,0,1546,91130,0,0,540,12578,0,0;QS=3,0;MQSB=0.99881;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,18,165:6:0	0,12,121:4:0
+X	1932	.	T	<*>	0	.	DP=27;I16=14,13,0,0,998,38154,0,0,1546,91130,0,0,541,12605,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,15,143:5:0	0,15,146:5:0
+X	1933	.	T	<*>	0	.	DP=27;I16=14,13,0,0,962,35344,0,0,1546,91130,0,0,542,12602,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,15,142:5:0	0,15,158:5:0
+X	1934	.	G	<*>	0	.	DP=27;I16=13,13,0,0,987,38219,0,0,1529,90841,0,0,543,12569,0,0;QS=3,0;MQSB=0.945959;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,15,134:5:0	0,15,143:5:0
+X	1935	.	C	<*>	0	.	DP=27;I16=14,12,0,0,963,36627,0,0,1529,90841,0,0,520,11930,0,0;QS=3,0;MQSB=0.937241;MQ0F=0	PL:DP:DV	0,45,255:15:0	0,18,162:6:0	0,15,154:5:0
+X	1936	.	C	<*>	0	.	DP=27;I16=14,13,0,0,1018,39406,0,0,1589,94441,0,0,547,12561,0,0;QS=3,0;MQSB=0.94394;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,18,177:6:0	0,15,159:5:0
+X	1937	.	T	<*>	0	.	DP=27;I16=14,13,0,0,1036,40636,0,0,1589,94441,0,0,547,12489,0,0;QS=3,0;MQSB=0.94394;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,18,182:6:0	0,15,170:5:0
+X	1938	.	G	<*>	0	.	DP=27;I16=14,13,0,0,1001,38377,0,0,1589,94441,0,0,546,12392,0,0;QS=3,0;MQSB=0.94394;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,18,166:6:0	0,15,155:5:0
+X	1939	.	T	<*>	0	.	DP=27;I16=14,12,0,0,964,36430,0,0,1560,93600,0,0,525,11909,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,18,167:6:0	0,12,144:4:0
+X	1940	.	G	<*>	0	.	DP=27;I16=14,13,0,0,1003,37937,0,0,1589,94441,0,0,542,12172,0,0;QS=3,0;MQSB=0.94394;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,18,159:6:0	0,15,155:5:0
+X	1941	.	G	<*>	0	.	DP=27;I16=14,13,0,0,1004,38072,0,0,1589,94441,0,0,540,12098,0,0;QS=3,0;MQSB=0.94394;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,18,176:6:0	0,15,156:5:0
+X	1942	.	C	<*>	0	.	DP=27;I16=14,12,0,0,996,38790,0,0,1560,93600,0,0,516,11564,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,18,174:6:0	0,12,140:4:0
+X	1943	.	T	<*>	0	.	DP=27;I16=14,13,0,0,1044,40952,0,0,1589,94441,0,0,536,12022,0,0;QS=3,0;MQSB=0.94394;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,18,184:6:0	0,15,167:5:0
+X	1944	.	T	<*>	0	.	DP=27;I16=14,13,0,0,987,37237,0,0,1589,94441,0,0,533,11971,0,0;QS=3,0;MQSB=0.94394;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,18,175:6:0	0,15,170:5:0
+X	1945	.	T	<*>	0	.	DP=27;I16=14,13,0,0,993,37067,0,0,1589,94441,0,0,530,11946,0,0;QS=3,0;MQSB=0.94394;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,18,174:6:0	0,15,171:5:0
+X	1946	.	G	<*>	0	.	DP=27;I16=14,13,0,0,1013,38617,0,0,1589,94441,0,0,526,11896,0,0;QS=3,0;MQSB=0.94394;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,18,162:6:0	0,15,162:5:0
+X	1947	.	A	<*>	0	.	DP=26;I16=13,13,0,0,950,35522,0,0,1529,90841,0,0,522,11818,0,0;QS=3,0;MQSB=0.945959;MQ0F=0	PL:DP:DV	0,45,255:15:0	0,18,167:6:0	0,15,160:5:0
+X	1948	.	G	C,<*>	0	.	DP=27;I16=14,12,0,1,966,36912,16,256,1560,93600,29,841,493,11135,25,625;QS=2.90361,0.0963855,0;SGB=-0.556633;RPB=1;MQB=1;MQSB=0.94394;BQB=1;MQ0F=0	PL:DP:DV	0,45,255,45,255,255:15:0	0,21,190,21,190,190:7:0	1,0,123,13,126,132:5:1
+X	1949	.	A	<*>	0	.	DP=26;I16=14,11,0,0,871,31325,0,0,1469,87241,0,0,490,11048,0,0;QS=3,0;MQSB=0.929204;MQ0F=0	PL:DP:DV	0,39,255:13:0	0,21,174:7:0	0,15,155:5:0
+X	1950	.	A	<*>	0	.	DP=27;I16=14,13,0,0,1007,38049,0,0,1589,94441,0,0,511,11559,0,0;QS=3,0;MQSB=0.94394;MQ0F=0	PL:DP:DV	0,42,255:14:0	0,21,205:7:0	0,18,176:6:0
+X	1951	.	G	<*>	0	.	DP=27;I16=14,13,0,0,960,35536,0,0,1589,94441,0,0,509,11469,0,0;QS=3,0;MQSB=0.94394;MQ0F=0	PL:DP:DV	0,42,255:14:0	0,21,180:7:0	0,18,181:6:0
+X	1952	.	A	<*>	0	.	DP=27;I16=14,12,0,0,924,33366,0,0,1529,90841,0,0,483,10779,0,0;QS=3,0;MQSB=0.937241;MQ0F=0	PL:DP:DV	0,39,255:13:0	0,21,184:7:0	0,18,182:6:0
+X	1953	.	A	<*>	0	.	DP=28;I16=15,12,0,0,925,32719,0,0,1589,94441,0,0,482,10740,0,0;QS=3,0;MQSB=0.935229;MQ0F=0	PL:DP:DV	0,42,255:14:0	0,21,189:7:0	0,18,168:6:0
+X	1954	.	A	C,<*>	0	.	DP=29;I16=14,13,0,1,929,33219,18,324,1620,97200,29,841,475,10679,25,625;QS=2.90217,0.0978261,0;SGB=-0.556633;RPB=1;MQB=1;MQSB=0.949591;BQB=1;MQ0F=0	PL:DP:DV	0,45,255,45,255,255:15:0	0,21,198,21,198,198:7:0	0,0,130,15,133,141:6:1
+X	1955	.	C	<*>	0	.	DP=29;I16=14,12,0,0,961,36067,0,0,1560,93600,0,0,451,10035,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,42,255:14:0	0,21,206:7:0	0,15,165:5:0
+X	1956	.	C	<*>	0	.	DP=29;I16=14,13,0,0,964,35402,0,0,1620,97200,0,0,475,10573,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,45,255:15:0	0,21,196:7:0	0,15,164:5:0
+X	1957	.	C	<*>	0	.	DP=29;I16=14,13,0,0,980,36212,0,0,1620,97200,0,0,472,10420,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,45,255:15:0	0,21,183:7:0	0,15,167:5:0
+X	1958	.	C	<*>	0	.	DP=29;I16=15,13,0,0,1003,37293,0,0,1649,98041,0,0,493,10825,0,0;QS=3,0;MQSB=0.942064;MQ0F=0	PL:DP:DV	0,45,255:15:0	0,21,191:7:0	0,18,190:6:0
+X	1959	.	T	<*>	0	.	DP=29;I16=16,13,0,0,1112,43258,0,0,1709,101641,0,0,491,10593,0,0;QS=3,0;MQSB=0.940317;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,21,213:7:0	0,18,193:6:0
+X	1960	.	T	<*>	0	.	DP=30;I16=17,13,0,0,1053,37939,0,0,1769,105241,0,0,485,10339,0,0;QS=3,0;MQSB=0.938685;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,21,196:7:0	0,18,186:6:0
+X	1961	.	C	<*>	0	.	DP=30;I16=17,13,0,0,1101,41737,0,0,1769,105241,0,0,480,10122,0,0;QS=3,0;MQSB=0.938685;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,21,195:7:0	0,18,183:6:0
+X	1962	.	T	<*>	0	.	DP=29;I16=17,12,0,0,1134,44582,0,0,1709,101641,0,0,477,9941,0,0;QS=3,0;MQSB=0.931617;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,21,208:7:0	0,18,198:6:0
+X	1963	.	G	<*>	0	.	DP=28;I16=16,12,0,0,1066,41050,0,0,1649,98041,0,0,476,9794,0,0;QS=3,0;MQSB=0.933359;MQ0F=0	PL:DP:DV	0,45,255:15:0	0,21,192:7:0	0,18,188:6:0
+X	1964	.	G	<*>	0	.	DP=28;I16=16,12,0,0,970,34764,0,0,1649,98041,0,0,475,9681,0,0;QS=3,0;MQSB=0.933359;MQ0F=0	PL:DP:DV	0,45,255:15:0	0,21,178:7:0	0,18,169:6:0
+X	1965	.	T	<*>	0	.	DP=29;I16=16,12,0,0,964,34772,0,0,1649,98041,0,0,449,8977,0,0;QS=3,0;MQSB=0.933359;MQ0F=0	PL:DP:DV	0,45,255:15:0	0,21,196:7:0	0,18,171:6:0
+X	1966	.	T	<*>	0	.	DP=29;I16=16,13,0,0,1029,37027,0,0,1709,101641,0,0,474,9558,0,0;QS=3,0;MQSB=0.940317;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,21,191:7:0	0,18,181:6:0
+X	1967	.	A	<*>	0	.	DP=29;I16=16,13,0,0,1030,37234,0,0,1709,101641,0,0,474,9550,0,0;QS=3,0;MQSB=0.940317;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,21,187:7:0	0,18,182:6:0
+X	1968	.	T	<*>	0	.	DP=29;I16=16,13,0,0,1075,40173,0,0,1709,101641,0,0,474,9578,0,0;QS=3,0;MQSB=0.940317;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,21,195:7:0	0,18,190:6:0
+X	1969	.	A	<*>	0	.	DP=28;I16=16,12,0,0,992,35828,0,0,1649,98041,0,0,474,9592,0,0;QS=3,0;MQSB=0.933359;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,18,175:6:0	0,18,186:6:0
+X	1970	.	C	<*>	0	.	DP=28;I16=16,12,0,0,1015,37503,0,0,1649,98041,0,0,474,9642,0,0;QS=3,0;MQSB=0.933359;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,18,170:6:0	0,18,180:6:0
+X	1971	.	A	<*>	0	.	DP=29;I16=16,13,0,0,1073,40273,0,0,1709,101641,0,0,474,9728,0,0;QS=3,0;MQSB=0.940317;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,18,178:6:0	0,21,206:7:0
+X	1972	.	T	<*>	0	.	DP=30;I16=16,14,0,0,1068,38978,0,0,1769,105241,0,0,475,9851,0,0;QS=3,0;MQSB=0.946202;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,18,176:6:0	0,21,203:7:0
+X	1973	.	A	<*>	0	.	DP=30;I16=16,13,0,0,1046,38070,0,0,1740,104400,0,0,452,9388,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,18,172:6:0	0,18,196:6:0
+X	1974	.	A	<*>	0	.	DP=29;I16=16,13,0,0,1086,41474,0,0,1709,101641,0,0,477,10065,0,0;QS=3,0;MQSB=0.940317;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,15,157:5:0	0,21,214:7:0
+X	1975	.	G	<*>	0	.	DP=28;I16=16,12,0,0,1067,41171,0,0,1649,98041,0,0,478,10156,0,0;QS=3,0;MQSB=0.933359;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,12,133:4:0	0,21,195:7:0
+X	1976	.	A	<*>	0	.	DP=28;I16=16,12,0,0,981,34839,0,0,1649,98041,0,0,478,10234,0,0;QS=3,0;MQSB=0.933359;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,12,125:4:0	0,21,199:7:0
+X	1977	.	C	<*>	0	.	DP=28;I16=16,12,0,0,1009,37471,0,0,1649,98041,0,0,477,10297,0,0;QS=3,0;MQSB=0.933359;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,12,132:4:0	0,21,194:7:0
+X	1978	.	A	<*>	0	.	DP=28;I16=16,12,0,0,1082,42132,0,0,1649,98041,0,0,476,10394,0,0;QS=3,0;MQSB=0.933359;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,12,144:4:0	0,21,220:7:0
+X	1979	.	G	<*>	0	.	DP=28;I16=16,11,0,0,1019,38927,0,0,1589,94441,0,0,454,10064,0,0;QS=3,0;MQSB=0.925036;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,12,122:4:0	0,21,208:7:0
+X	1980	.	C	<*>	0	.	DP=27;I16=16,10,0,0,932,34456,0,0,1529,90841,0,0,452,10114,0,0;QS=3,0;MQSB=0.914947;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,9,107:3:0	0,21,197:7:0
+X	1981	.	C	<*>	0	.	DP=28;I16=16,12,0,0,998,36510,0,0,1649,98041,0,0,469,10479,0,0;QS=3,0;MQSB=0.933359;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,9,101:3:0	0,24,219:8:0
+X	1982	.	A	<*>	0	.	DP=29;I16=16,12,0,0,1035,38815,0,0,1649,98041,0,0,472,10548,0,0;QS=3,0;MQSB=0.933359;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,9,110:3:0	0,27,254:9:0
+X	1983	.	G	<*>	0	.	DP=28;I16=16,12,0,0,1048,40322,0,0,1649,98041,0,0,477,10599,0,0;QS=3,0;MQSB=0.933359;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,9,96:3:0	0,27,249:9:0
+X	1984	.	A	<*>	0	.	DP=27;I16=16,11,0,0,1024,39232,0,0,1589,94441,0,0,482,10632,0,0;QS=3,0;MQSB=0.925036;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,6,70:2:0	0,27,255:9:0
+X	1985	.	G	<*>	0	.	DP=27;I16=16,11,0,0,1009,38449,0,0,1589,94441,0,0,487,10695,0,0;QS=3,0;MQSB=0.925036;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,6,66:2:0	0,27,231:9:0
+X	1986	.	A	<*>	0	.	DP=27;I16=16,10,0,0,926,33696,0,0,1560,93600,0,0,466,10112,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,6,76:2:0	0,24,223:8:0
+X	1987	.	A	<*>	0	.	DP=28;I16=17,11,0,0,1034,39088,0,0,1649,98041,0,0,495,10807,0,0;QS=3,0;MQSB=0.923174;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,6,78:2:0	0,27,247:9:0
+X	1988	.	G	<*>	0	.	DP=28;I16=17,11,0,0,1050,39980,0,0,1649,98041,0,0,499,10855,0,0;QS=3,0;MQSB=0.923174;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,6,63:2:0	0,27,239:9:0
+X	1989	.	G	<*>	0	.	DP=28;I16=17,10,0,0,994,37610,0,0,1589,94441,0,0,493,10801,0,0;QS=3,0;MQSB=0.912952;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,6,73:2:0	0,27,237:9:0
+X	1990	.	G	T,<*>	0	.	DP=28;I16=17,9,0,1,965,36359,33,1089,1560,93600,29,841,472,10250,25,625;QS=2.90675,0.0932476,0;SGB=-0.556633;RPB=1;MQB=1;MQSB=0.912952;BQB=1;MQ0F=0	PL:DP:DV	0,48,255,48,255,255:16:0	0,6,71,6,71,71:2:0	2,0,195,26,198,215:9:1
+X	1991	.	A	<*>	0	.	DP=28;I16=17,11,0,0,1017,38203,0,0,1649,98041,0,0,507,10975,0,0;QS=3,0;MQSB=0.923174;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,6,60:2:0	0,27,250:9:0
+X	1992	.	G	<*>	0	.	DP=28;I16=17,11,0,0,1028,38852,0,0,1649,98041,0,0,509,11039,0,0;QS=3,0;MQSB=0.923174;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,6,62:2:0	0,27,231:9:0
+X	1993	.	T	<*>	0	.	DP=28;I16=17,11,0,0,1015,37325,0,0,1649,98041,0,0,511,11131,0,0;QS=3,0;MQSB=0.923174;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,6,59:2:0	0,27,243:9:0
+X	1994	.	T	<*>	0	.	DP=27;I16=16,11,0,0,942,33698,0,0,1589,94441,0,0,514,11250,0,0;QS=3,0;MQSB=0.925036;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,6,54:2:0	0,24,216:8:0
+X	1995	.	G	<*>	0	.	DP=28;I16=16,11,0,0,960,35432,0,0,1620,97200,0,0,492,10770,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,54,255:18:0	0,6,66:2:0	0,21,188:7:0
+X	1996	.	C	<*>	0	.	DP=29;I16=17,12,0,0,1022,37426,0,0,1709,101641,0,0,519,11469,0,0;QS=3,0;MQSB=0.931617;MQ0F=0	PL:DP:DV	0,57,255:19:0	0,6,64:2:0	0,24,192:8:0
+X	1997	.	C	<*>	0	.	DP=29;I16=17,11,0,0,934,32858,0,0,1649,98041,0,0,520,11524,0,0;QS=3,0;MQSB=0.923174;MQ0F=0	PL:DP:DV	0,54,255:18:0	0,6,70:2:0	0,24,193:8:0
+X	1998	.	C	<*>	0	.	DP=29;I16=17,12,0,0,1027,37843,0,0,1709,101641,0,0,522,11562,0,0;QS=3,0;MQSB=0.931617;MQ0F=0	PL:DP:DV	0,57,255:19:0	0,6,69:2:0	0,24,222:8:0
+X	1999	.	A	<*>	0	.	DP=28;I16=17,11,0,0,1073,41493,0,0,1649,98041,0,0,525,11627,0,0;QS=3,0;MQSB=0.923174;MQ0F=0	PL:DP:DV	0,57,255:19:0	0,6,72:2:0	0,21,206:7:0
+X	2000	.	G	<*>	0	.	DP=28;I16=16,11,0,0,1036,40576,0,0,1589,94441,0,0,511,11395,0,0;QS=3,0;MQSB=0.925036;MQ0F=0	PL:DP:DV	0,57,255:19:0	0,6,72:2:0	0,18,168:6:0
+X	2001	.	G	<*>	0	.	DP=28;I16=15,11,0,0,955,35661,0,0,1529,90841,0,0,489,10853,0,0;QS=3,0;MQSB=0.927041;MQ0F=0	PL:DP:DV	0,54,255:18:0	0,6,62:2:0	0,18,172:6:0
+X	2002	.	G	<*>	0	.	DP=28;I16=17,10,0,0,907,32227,0,0,1620,97200,0,0,519,11663,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,57,255:19:0	0,6,53:2:0	0,18,163:6:0
+X	2003	.	T	<*>	0	.	DP=28;I16=17,11,0,0,920,31866,0,0,1649,98041,0,0,541,12163,0,0;QS=3,0;MQSB=0.923174;MQ0F=0	PL:DP:DV	0,57,255:19:0	0,6,49:2:0	0,21,190:7:0
+X	2004	.	G	<*>	0	.	DP=27;I16=16,10,0,0,970,36928,0,0,1560,93600,0,0,530,12110,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,54,255:18:0	0,6,57:2:0	0,18,178:6:0
+X	2005	.	G	<*>	0	.	DP=27;I16=16,10,0,0,868,30936,0,0,1560,93600,0,0,536,12370,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,54,255:18:0	0,6,59:2:0	0,18,153:6:0
+X	2006	.	C	<*>	0	.	DP=27;I16=16,10,0,0,968,37046,0,0,1560,93600,0,0,541,12605,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,54,255:18:0	0,6,73:2:0	0,18,166:6:0
+X	2007	.	A	<*>	0	.	DP=27;I16=16,11,0,0,1000,37396,0,0,1589,94441,0,0,556,12882,0,0;QS=3,0;MQSB=0.925036;MQ0F=0	PL:DP:DV	0,54,255:18:0	0,6,76:2:0	0,21,193:7:0
+X	2008	.	C	<*>	0	.	DP=26;I16=16,10,0,0,964,36892,0,0,1529,90841,0,0,555,12833,0,0;QS=3,0;MQSB=0.914947;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,6,73:2:0	0,21,183:7:0
+X	2009	.	A	<*>	0	.	DP=26;I16=16,10,0,0,997,38955,0,0,1529,90841,0,0,554,12802,0,0;QS=3,0;MQSB=0.914947;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,6,74:2:0	0,21,210:7:0
+X	2010	.	G	<*>	0	.	DP=26;I16=16,9,0,0,936,36208,0,0,1500,90000,0,0,542,12640,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,6,73:2:0	0,18,169:6:0
+X	2011	.	C	<*>	0	.	DP=26;I16=16,9,0,0,966,37960,0,0,1500,90000,0,0,541,12617,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,6,74:2:0	0,18,175:6:0
+X	2012	.	A	<*>	0	.	DP=27;I16=16,11,0,0,956,35018,0,0,1589,94441,0,0,548,12676,0,0;QS=3,0;MQSB=0.925036;MQ0F=0	PL:DP:DV	0,54,255:18:0	0,6,74:2:0	0,21,189:7:0
+X	2013	.	C	<*>	0	.	DP=27;I16=15,10,0,0,876,31370,0,0,1500,90000,0,0,514,11950,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,6,69:2:0	0,18,160:6:0
+X	2014	.	G	<*>	0	.	DP=27;I16=17,10,0,0,903,31239,0,0,1589,94441,0,0,545,12591,0,0;QS=3,0;MQSB=0.912952;MQ0F=0	PL:DP:DV	0,54,255:18:0	0,9,80:3:0	0,18,160:6:0
+X	2015	.	T	<*>	0	.	DP=27;I16=17,10,0,0,999,37507,0,0,1589,94441,0,0,545,12577,0,0;QS=3,0;MQSB=0.912952;MQ0F=0	PL:DP:DV	0,54,255:18:0	0,9,95:3:0	0,18,178:6:0
+X	2016	.	T	<*>	0	.	DP=27;I16=17,10,0,0,971,35649,0,0,1589,94441,0,0,545,12583,0,0;QS=3,0;MQSB=0.912952;MQ0F=0	PL:DP:DV	0,54,255:18:0	0,9,93:3:0	0,18,178:6:0
+X	2017	.	G	<*>	0	.	DP=28;I16=17,11,0,0,1013,37849,0,0,1649,98041,0,0,545,12609,0,0;QS=3,0;MQSB=0.923174;MQ0F=0	PL:DP:DV	0,57,255:19:0	0,9,91:3:0	0,18,172:6:0
+X	2018	.	C	<*>	0	.	DP=28;I16=17,11,0,0,1060,41414,0,0,1649,98041,0,0,546,12656,0,0;QS=3,0;MQSB=0.923174;MQ0F=0	PL:DP:DV	0,57,255:19:0	0,9,97:3:0	0,18,169:6:0
+X	2019	.	T	<*>	0	.	DP=28;I16=17,11,0,0,1083,42253,0,0,1649,98041,0,0,547,12725,0,0;QS=3,0;MQSB=0.923174;MQ0F=0	PL:DP:DV	0,57,255:19:0	0,9,106:3:0	0,18,187:6:0
+X	2020	.	G	<*>	0	.	DP=29;I16=18,11,0,0,1095,42063,0,0,1678,98882,0,0,548,12816,0,0;QS=3,0;MQSB=0.987702;MQ0F=0	PL:DP:DV	0,60,255:20:0	0,9,85:3:0	0,18,175:6:0
+X	2021	.	C	<*>	0	.	DP=29;I16=18,11,0,0,1081,41535,0,0,1709,101641,0,0,551,12877,0,0;QS=3,0;MQSB=0.969907;MQ0F=0	PL:DP:DV	0,63,255:21:0	0,9,97:3:0	0,15,167:5:0
+X	2022	.	C	<*>	0	.	DP=30;I16=19,11,0,0,1115,42003,0,0,1769,105241,0,0,555,12907,0,0;QS=3,0;MQSB=0.972375;MQ0F=0	PL:DP:DV	0,63,255:21:0	0,9,92:3:0	0,18,177:6:0
+X	2023	.	A	<*>	0	.	DP=30;I16=19,10,0,0,1063,39991,0,0,1709,101641,0,0,549,12837,0,0;QS=3,0;MQSB=0.974027;MQ0F=0	PL:DP:DV	0,60,255:20:0	0,9,96:3:0	0,18,186:6:0
+X	2024	.	G	<*>	0	.	DP=32;I16=20,12,0,0,1168,43872,0,0,1889,112441,0,0,564,12982,0,0;QS=3,0;MQSB=0.973096;MQ0F=0	PL:DP:DV	0,63,255:21:0	0,9,92:3:0	0,24,203:8:0
+X	2025	.	T	<*>	0	.	DP=32;I16=20,12,0,0,1150,42122,0,0,1889,112441,0,0,569,12981,0,0;QS=3,0;MQSB=0.973096;MQ0F=0	PL:DP:DV	0,63,255:21:0	0,9,87:3:0	0,24,226:8:0
+X	2026	.	T	<*>	0	.	DP=32;I16=20,12,0,0,1130,40724,0,0,1889,112441,0,0,572,12908,0,0;QS=3,0;MQSB=0.973096;MQ0F=0	PL:DP:DV	0,63,255:21:0	0,9,94:3:0	0,24,208:8:0
+X	2027	.	A	<*>	0	.	DP=32;I16=19,12,0,0,1121,40871,0,0,1829,108841,0,0,550,12240,0,0;QS=3,0;MQSB=0.970829;MQ0F=0	PL:DP:DV	0,63,255:21:0	0,9,84:3:0	0,21,207:7:0
+X	2028	.	C	<*>	0	.	DP=32;I16=20,12,0,0,1242,48548,0,0,1889,112441,0,0,577,12803,0,0;QS=3,0;MQSB=0.973096;MQ0F=0	PL:DP:DV	0,63,255:21:0	0,9,94:3:0	0,24,228:8:0
+X	2029	.	T	<*>	0	.	DP=32;I16=20,12,0,0,1229,47605,0,0,1889,112441,0,0,578,12724,0,0;QS=3,0;MQSB=0.973096;MQ0F=0	PL:DP:DV	0,63,255:21:0	0,9,102:3:0	0,24,236:8:0
+X	2030	.	G	<*>	0	.	DP=32;I16=20,12,0,0,1222,47140,0,0,1889,112441,0,0,579,12679,0,0;QS=3,0;MQSB=0.973096;MQ0F=0	PL:DP:DV	0,63,255:21:0	0,9,93:3:0	0,24,216:8:0
+X	2031	.	C	<*>	0	.	DP=31;I16=19,12,0,0,1150,43656,0,0,1829,108841,0,0,581,12667,0,0;QS=3,0;MQSB=0.970829;MQ0F=0	PL:DP:DV	0,60,255:20:0	0,9,96:3:0	0,24,204:8:0
+X	2032	.	C	<*>	0	.	DP=31;I16=19,12,0,0,1157,44035,0,0,1829,108841,0,0,583,12687,0,0;QS=3,0;MQSB=0.970829;MQ0F=0	PL:DP:DV	0,60,255:20:0	0,9,90:3:0	0,24,210:8:0
+X	2033	.	A	<*>	0	.	DP=30;I16=19,11,0,0,1091,40223,0,0,1769,105241,0,0,585,12689,0,0;QS=3,0;MQSB=0.972375;MQ0F=0	PL:DP:DV	0,60,255:20:0	0,9,93:3:0	0,21,203:7:0
+X	2034	.	T	<*>	0	.	DP=30;I16=19,11,0,0,1104,41498,0,0,1769,105241,0,0,587,12723,0,0;QS=3,0;MQSB=0.972375;MQ0F=0	PL:DP:DV	0,60,255:20:0	0,9,91:3:0	0,21,208:7:0
+X	2035	.	T	<*>	0	.	DP=29;I16=18,11,0,0,1084,41024,0,0,1709,101641,0,0,589,12739,0,0;QS=3,0;MQSB=0.969907;MQ0F=0	PL:DP:DV	0,60,255:20:0	0,6,69:2:0	0,21,211:7:0
+X	2036	.	T	<*>	0	.	DP=29;I16=18,11,0,0,1080,40612,0,0,1709,101641,0,0,591,12787,0,0;QS=3,0;MQSB=0.969907;MQ0F=0	PL:DP:DV	0,60,255:20:0	0,6,67:2:0	0,21,216:7:0
+X	2037	.	T	<*>	0	.	DP=29;I16=18,11,0,0,1082,40956,0,0,1709,101641,0,0,592,12818,0,0;QS=3,0;MQSB=0.969907;MQ0F=0	PL:DP:DV	0,60,255:20:0	0,6,69:2:0	0,21,217:7:0
+X	2038	.	C	<*>	0	.	DP=29;I16=18,11,0,0,1117,43573,0,0,1709,101641,0,0,592,12832,0,0;QS=3,0;MQSB=0.969907;MQ0F=0	PL:DP:DV	0,60,255:20:0	0,6,69:2:0	0,21,211:7:0
+X	2039	.	A	<*>	0	.	DP=29;I16=18,11,0,0,1067,39581,0,0,1709,101641,0,0,592,12878,0,0;QS=3,0;MQSB=0.969907;MQ0F=0	PL:DP:DV	0,60,255:20:0	0,6,72:2:0	0,21,212:7:0
+X	2040	.	C	<*>	0	.	DP=29;I16=18,11,0,0,1077,40469,0,0,1709,101641,0,0,590,12856,0,0;QS=3,0;MQSB=0.969907;MQ0F=0	PL:DP:DV	0,60,255:20:0	0,6,69:2:0	0,21,196:7:0
+X	2041	.	G	A,<*>	0	.	DP=31;I16=6,5,12,7,389,14023,721,28149,660,39600,1109,65641,235,5607,353,7259;QS=0.917304,2.0827,0;VDB=0.816435;SGB=-4.18892;RPB=0.88473;MQB=0.972375;MQSB=0.968257;BQB=0.311275;MQ0F=0	PL:DP:DV	229,0,212,255,245,255:21:11	32,0,24,35,27,59:2:1	223,21,0,223,21,223:7:7
+X	2042	.	G	<*>	0	.	DP=32;I16=18,14,0,0,1189,45617,0,0,1889,112441,0,0,588,12910,0,0;QS=3,0;MQSB=0.965264;MQ0F=0	PL:DP:DV	0,66,255:22:0	0,9,86:3:0	0,21,206:7:0
+X	2043	.	G	<*>	0	.	DP=32;I16=17,14,0,0,1115,41585,0,0,1829,108841,0,0,581,12891,0,0;QS=3,0;MQSB=0.962133;MQ0F=0	PL:DP:DV	0,63,255:21:0	0,9,90:3:0	0,21,197:7:0
+X	2044	.	C	<*>	0	.	DP=32;I16=18,14,0,0,1213,47029,0,0,1889,112441,0,0,588,13006,0,0;QS=3,0;MQSB=0.965264;MQ0F=0	PL:DP:DV	0,66,255:22:0	0,9,85:3:0	0,21,207:7:0
+X	2045	.	A	<*>	0	.	DP=32;I16=18,14,0,0,1181,44527,0,0,1889,112441,0,0,588,13108,0,0;QS=3,0;MQSB=0.965264;MQ0F=0	PL:DP:DV	0,66,255:22:0	0,9,83:3:0	0,21,213:7:0
+X	2046	.	T	<*>	0	.	DP=32;I16=18,14,0,0,1197,45135,0,0,1889,112441,0,0,587,13195,0,0;QS=3,0;MQSB=0.965264;MQ0F=0	PL:DP:DV	0,66,255:22:0	0,9,103:3:0	0,21,216:7:0
+X	2047	.	G	<*>	0	.	DP=34;I16=17,16,0,0,1248,47798,0,0,1949,116041,0,0,557,12491,0,0;QS=3,0;MQSB=0.959328;MQ0F=0	PL:DP:DV	0,72,255:24:0	0,9,88:3:0	0,18,195:6:0
+X	2048	.	A	<*>	0	.	DP=34;I16=18,16,0,0,1230,45184,0,0,2009,119641,0,0,578,13022,0,0;QS=3,0;MQSB=0.962621;MQ0F=0	PL:DP:DV	0,72,255:24:0	0,9,87:3:0	0,21,206:7:0
+X	2049	.	A	<*>	0	.	DP=33;I16=17,16,0,0,1207,44567,0,0,1949,116041,0,0,575,12963,0,0;QS=3,0;MQSB=0.959328;MQ0F=0	PL:DP:DV	0,72,255:24:0	0,6,74:2:0	0,21,208:7:0
+X	2050	.	A	<*>	0	.	DP=33;I16=16,16,0,0,1169,43313,0,0,1889,112441,0,0,545,12211,0,0;QS=3,0;MQSB=0.955563;MQ0F=0	PL:DP:DV	0,72,255:24:0	0,6,77:2:0	0,18,188:6:0
+X	2051	.	T	<*>	0	.	DP=31;I16=16,15,0,0,1134,42164,0,0,1829,108841,0,0,567,12737,0,0;QS=3,0;MQSB=0.957006;MQ0F=0	PL:DP:DV	0,69,255:23:0	0,6,69:2:0	0,18,170:6:0
+X	2052	.	G	<*>	0	.	DP=31;I16=16,15,0,0,1180,45546,0,0,1829,108841,0,0,564,12664,0,0;QS=3,0;MQSB=0.957006;MQ0F=0	PL:DP:DV	0,69,255:23:0	0,6,74:2:0	0,18,175:6:0
+X	2053	.	G	T,<*>	0	.	DP=31;I16=15,15,0,1,1126,42672,23,529,1769,105241,60,3600,537,11991,25,625;QS=2.97307,0.0269321,0;SGB=-0.556633;RPB=1;MQB=1;MQSB=0.951229;BQB=1;MQ0F=0	PL:DP:DV	0,46,255,66,255,255:23:1	0,6,71,6,71,71:2:0	0,18,180,18,180,180:6:0
+X	2054	.	A	<*>	0	.	DP=30;I16=15,15,0,0,1123,43027,0,0,1769,105241,0,0,562,12592,0,0;QS=3,0;MQSB=0.952765;MQ0F=0	PL:DP:DV	0,66,255:22:0	0,6,78:2:0	0,18,171:6:0
+X	2055	.	G	<*>	0	.	DP=30;I16=15,15,0,0,1156,45206,0,0,1769,105241,0,0,562,12592,0,0;QS=3,0;MQSB=0.952765;MQ0F=0	PL:DP:DV	0,66,255:22:0	0,6,66:2:0	0,18,168:6:0
+X	2056	.	A	<*>	0	.	DP=30;I16=15,15,0,0,1124,42416,0,0,1769,105241,0,0,560,12518,0,0;QS=3,0;MQSB=0.952765;MQ0F=0	PL:DP:DV	0,66,255:22:0	0,6,71:2:0	0,18,179:6:0
+X	2057	.	T	<*>	0	.	DP=30;I16=15,15,0,0,1094,40082,0,0,1769,105241,0,0,556,12374,0,0;QS=3,0;MQSB=0.952765;MQ0F=0	PL:DP:DV	0,66,255:22:0	0,6,72:2:0	0,18,178:6:0
+X	2058	.	A	<*>	0	.	DP=29;I16=14,15,0,0,1035,37517,0,0,1709,101641,0,0,552,12212,0,0;QS=3,0;MQSB=0.947838;MQ0F=0	PL:DP:DV	0,63,255:21:0	0,6,57:2:0	0,18,179:6:0
+X	2059	.	A	<*>	0	.	DP=29;I16=14,15,0,0,1063,39615,0,0,1709,101641,0,0,548,12082,0,0;QS=3,0;MQSB=0.947838;MQ0F=0	PL:DP:DV	0,63,255:21:0	0,6,66:2:0	0,18,188:6:0
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+X	3212	.	T	<*>	0	.	DP=17;I16=10,6,0,0,575,21295,0,0,960,57600,0,0,316,6964,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,27,222:9:0	0,9,100:3:0	0,12,144:4:0
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+X	3226	.	T	<*>	0	.	DP=18;I16=11,6,0,0,582,20466,0,0,1020,61200,0,0,282,5996,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,27,224:9:0	0,12,112:4:0	0,12,131:4:0
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+X	3230	.	T	<*>	0	.	DP=19;I16=12,6,0,0,669,25441,0,0,1049,62041,0,0,261,5187,0,0;QS=3,0;MQSB=0.961295;MQ0F=0	PL:DP:DV	0,33,255:11:0	0,9,107:3:0	0,12,139:4:0
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+X	3242	.	T	<*>	0	.	DP=19;I16=12,7,0,0,655,23279,0,0,1140,68400,0,0,277,5911,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,30,252:10:0	0,12,104:4:0	0,15,152:5:0
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+X	3251	.	T	<*>	0	.	DP=16;I16=10,6,0,0,585,22193,0,0,960,57600,0,0,319,7165,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,27,241:9:0	0,9,104:3:0	0,12,135:4:0
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+X	3253	.	T	<*>	0	.	DP=16;I16=10,6,0,0,589,21933,0,0,960,57600,0,0,323,7281,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,27,245:9:0	0,9,102:3:0	0,12,132:4:0
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+X	3587	.	G	A,<*>	0	.	DP=29;I16=4,7,10,6,426,16884,555,20381,660,39600,960,57600,192,4420,280,5942;QS=1.32665,1.67335,0;VDB=0.902044;SGB=-3.91326;RPB=0.800999;MQB=1;MQSB=1;BQB=0.156944;MQ0F=0	PL:DP:DV	161,0,184,182,205,255:14:7	22,0,118,34,121,148:5:1	212,24,0,212,24,212:8:8
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+X	3798	.	T	<*>	0	.	DP=27;I16=14,11,0,0,921,37161,0,0,1301,72235,0,0,430,9554,0,0;QS=3,0;MQSB=0.283586;MQ0F=0	PL:DP:DV	0,42,255:14:0	0,21,148:7:0	0,12,165:4:0
+X	3799	.	T	<*>	0	.	DP=27;I16=15,11,0,0,913,35929,0,0,1361,75835,0,0,439,9729,0,0;QS=3,0;MQSB=0.334895;MQ0F=0	PL:DP:DV	0,45,255:15:0	0,21,150:7:0	0,12,161:4:0
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+X	3801	.	T	<*>	0	.	DP=23;I16=12,10,0,0,804,33600,0,0,1121,61435,0,0,430,9750,0,0;QS=3,0;MQSB=0.217267;MQ0F=0	PL:DP:DV	0,42,255:14:0	0,15,99:5:0	0,9,133:3:0
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+X	3805	.	C	<*>	0	.	DP=22;I16=12,9,0,0,737,29243,0,0,1061,57835,0,0,428,9950,0,0;QS=3,0;MQSB=0.262932;MQ0F=0	PL:DP:DV	0,42,255:14:0	0,12,81:4:0	0,9,130:3:0
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+X	3807	.	C	<*>	0	.	DP=22;I16=10,9,0,0,664,25304,0,0,994,54486,0,0,377,8885,0,0;QS=3,0;MQSB=0.472367;MQ0F=0	PL:DP:DV	0,36,255:12:0	0,12,83:4:0	0,9,115:3:0
+X	3808	.	G	<*>	0	.	DP=21;I16=9,9,0,0,653,25297,0,0,957,53117,0,0,375,8873,0,0;QS=3,0;MQSB=0.597145;MQ0F=0	PL:DP:DV	0,33,233:11:0	0,12,109:4:0	0,9,132:3:0
+X	3809	.	T	<*>	0	.	DP=22;I16=11,10,0,0,779,32151,0,0,1084,60066,0,0,416,9810,0,0;QS=3,0;MQSB=0.285029;MQ0F=0	PL:DP:DV	0,39,249:13:0	0,12,115:4:0	0,12,161:4:0
+X	3810	.	C	<*>	0	.	DP=23;I16=9,11,0,0,811,34815,0,0,1077,60317,0,0,369,8739,0,0;QS=3,0;MQSB=0.499893;MQ0F=0	PL:DP:DV	0,36,255:12:0	0,12,112:4:0	0,12,153:4:0
+X	3811	.	A	C,<*>	0	.	DP=23;I16=9,11,2,0,777,32631,39,785,1077,60317,67,3349,367,8669,42,914;QS=2.94104,0.0589569,0;VDB=0.18;SGB=0.346553;RPB=0.425;MQB=0.25;MQSB=0.246128;BQB=0.025;MQ0F=0	PL:DP:DV	0,15,248,36,254,255:14:2	0,12,116,12,116,116:4:0	0,12,158,12,158,158:4:0
+X	3812	.	T	<*>	0	.	DP=23;I16=10,11,0,0,802,32860,0,0,1084,60066,0,0,405,9447,0,0;QS=3,0;MQSB=0.187115;MQ0F=0	PL:DP:DV	0,39,255:13:0	0,12,114:4:0	0,12,160:4:0
+X	3813	.	A	<*>	0	.	DP=22;I16=10,11,0,0,815,35077,0,0,1084,60066,0,0,402,9330,0,0;QS=3,0;MQSB=0.187115;MQ0F=0	PL:DP:DV	0,39,255:13:0	0,12,119:4:0	0,12,170:4:0
+X	3814	.	G	<*>	0	.	DP=21;I16=8,11,0,0,775,33731,0,0,1037,58597,0,0,375,8605,0,0;QS=3,0;MQSB=0.41781;MQ0F=0	PL:DP:DV	0,33,255:11:0	0,12,113:4:0	0,12,163:4:0
+X	3815	.	A	<*>	0	.	DP=20;I16=8,11,0,0,708,29130,0,0,1010,57328,0,0,397,9049,0,0;QS=3,0;MQSB=0.373354;MQ0F=0	PL:DP:DV	0,33,239:11:0	0,12,110:4:0	0,12,162:4:0
+X	3816	.	A	<*>	0	.	DP=20;I16=8,11,0,0,729,31027,0,0,1010,57328,0,0,395,8933,0,0;QS=3,0;MQSB=0.373354;MQ0F=0	PL:DP:DV	0,33,248:11:0	0,12,104:4:0	0,12,160:4:0
+X	3817	.	A	<*>	0	.	DP=20;I16=8,11,0,0,752,31580,0,0,1010,57328,0,0,393,8833,0,0;QS=3,0;MQSB=0.373354;MQ0F=0	PL:DP:DV	0,33,255:11:0	0,12,110:4:0	0,12,161:4:0
+X	3818	.	T	<*>	0	.	DP=20;I16=8,11,0,0,728,30466,0,0,1010,57328,0,0,391,8749,0,0;QS=3,0;MQSB=0.373354;MQ0F=0	PL:DP:DV	0,33,252:11:0	0,12,115:4:0	0,12,160:4:0
+X	3819	.	A	<*>	0	.	DP=21;I16=9,11,0,0,790,34094,0,0,1039,58169,0,0,389,8681,0,0;QS=3,0;MQSB=0.247381;MQ0F=0	PL:DP:DV	0,36,255:12:0	0,12,121:4:0	0,12,167:4:0
+X	3820	.	G	<*>	0	.	DP=21;I16=9,11,0,0,788,33636,0,0,1039,58169,0,0,388,8630,0,0;QS=3,0;MQSB=0.247381;MQ0F=0	PL:DP:DV	0,36,255:12:0	0,12,112:4:0	0,12,157:4:0
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+X	3822	.	G	<*>	0	.	DP=22;I16=10,11,0,0,810,33228,0,0,1099,61769,0,0,386,8532,0,0;QS=3,0;MQSB=0.317882;MQ0F=0	PL:DP:DV	0,39,255:13:0	0,12,103:4:0	0,12,157:4:0
+X	3823	.	T	<*>	0	.	DP=22;I16=9,11,0,0,753,30705,0,0,1042,58520,0,0,380,8460,0,0;QS=3,0;MQSB=0.434285;MQ0F=0	PL:DP:DV	0,36,255:12:0	0,12,102:4:0	0,12,163:4:0
+X	3824	.	C	<*>	0	.	DP=22;I16=10,11,0,0,802,32368,0,0,1099,61769,0,0,384,8456,0,0;QS=3,0;MQSB=0.317882;MQ0F=0	PL:DP:DV	0,39,255:13:0	0,12,105:4:0	0,12,159:4:0
+X	3825	.	C	<*>	0	.	DP=23;I16=10,11,0,0,813,33955,0,0,1079,59889,0,0,379,8387,0,0;QS=3,0;MQSB=0.317882;MQ0F=0	PL:DP:DV	0,36,255:12:0	0,15,130:5:0	0,12,157:4:0
+X	3826	.	T	<*>	0	.	DP=23;I16=11,11,0,0,827,34611,0,0,1136,63138,0,0,381,8357,0,0;QS=3,0;MQSB=0.232836;MQ0F=0	PL:DP:DV	0,39,255:13:0	0,15,133:5:0	0,12,155:4:0
+X	3827	.	G	<*>	0	.	DP=23;I16=11,10,0,0,820,34130,0,0,1076,59538,0,0,355,7715,0,0;QS=3,0;MQSB=0.269397;MQ0F=0	PL:DP:DV	0,39,255:13:0	0,12,121:4:0	0,12,162:4:0
+X	3828	.	C	<*>	0	.	DP=23;I16=11,10,0,0,805,33147,0,0,1076,59538,0,0,354,7720,0,0;QS=3,0;MQSB=0.269397;MQ0F=0	PL:DP:DV	0,39,255:13:0	0,12,114:4:0	0,12,157:4:0
+X	3829	.	A	<*>	0	.	DP=22;I16=9,11,0,0,763,31295,0,0,1069,59789,0,0,369,8241,0,0;QS=3,0;MQSB=0.477679;MQ0F=0	PL:DP:DV	0,33,255:11:0	0,15,132:5:0	0,12,158:4:0
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+X	3831	.	C	A,<*>	0	.	DP=23;I16=10,11,1,0,802,32198,14,196,1126,63038,10,100,370,8294,7,49;QS=2.97758,0.0224215,0;SGB=-0.556633;RPB=1;MQB=1;MQSB=0.232836;BQB=1;MQ0F=0	PL:DP:DV	0,27,255,36,255,255:13:1	0,15,134,15,134,134:5:0	0,12,149,12,149,149:4:0
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+X	3833	.	C	<*>	0	.	DP=23;I16=10,11,0,0,690,24938,0,0,1076,59538,0,0,377,8409,0,0;QS=3,0;MQSB=0.175325;MQ0F=0	PL:DP:DV	0,36,249:12:0	0,15,113:5:0	0,12,131:4:0
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+X	3839	.	C	<*>	0	.	DP=23;I16=9,13,0,0,688,22248,0,0,1132,61648,0,0,386,8238,0,0;QS=3,0;MQSB=0.248197;MQ0F=0	PL:DP:DV	0,36,255:12:0	0,18,123:6:0	0,12,112:4:0
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+X	3841	.	T	<*>	0	.	DP=23;I16=9,14,0,0,867,33103,0,0,1192,65248,0,0,414,8734,0,0;QS=3,0;MQSB=0.211072;MQ0F=0	PL:DP:DV	0,36,255:12:0	0,18,167:6:0	0,15,162:5:0
+X	3842	.	C	<*>	0	.	DP=23;I16=9,14,0,0,890,34728,0,0,1192,65248,0,0,415,8689,0,0;QS=3,0;MQSB=0.211072;MQ0F=0	PL:DP:DV	0,36,255:12:0	0,18,167:6:0	0,15,159:5:0
+X	3843	.	T	<*>	0	.	DP=24;I16=9,14,0,0,896,35122,0,0,1192,65248,0,0,416,8674,0,0;QS=3,0;MQSB=0.211072;MQ0F=0	PL:DP:DV	0,36,255:12:0	0,18,164:6:0	0,15,159:5:0
+X	3844	.	G	<*>	0	.	DP=26;I16=10,16,0,0,959,35715,0,0,1372,76048,0,0,442,9314,0,0;QS=3,0;MQSB=0.220358;MQ0F=0	PL:DP:DV	0,39,255:13:0	0,21,177:7:0	0,18,172:6:0
+X	3845	.	T	<*>	0	.	DP=26;I16=10,16,0,0,970,36442,0,0,1372,76048,0,0,444,9310,0,0;QS=3,0;MQSB=0.220358;MQ0F=0	PL:DP:DV	0,39,255:13:0	0,21,186:7:0	0,18,166:6:0
+X	3846	.	G	<*>	0	.	DP=27;I16=10,17,0,0,993,37297,0,0,1432,79648,0,0,446,9338,0,0;QS=3,0;MQSB=0.195223;MQ0F=0	PL:DP:DV	0,39,255:13:0	0,21,175:7:0	0,21,172:7:0
+X	3847	.	T	<*>	0	.	DP=27;I16=10,16,0,0,952,35268,0,0,1372,76048,0,0,423,8723,0,0;QS=3,0;MQSB=0.220358;MQ0F=0	PL:DP:DV	0,39,255:13:0	0,18,170:6:0	0,21,189:7:0
+X	3848	.	C	<*>	0	.	DP=27;I16=10,17,0,0,1025,39533,0,0,1432,79648,0,0,449,9341,0,0;QS=3,0;MQSB=0.195223;MQ0F=0	PL:DP:DV	0,39,255:13:0	0,21,177:7:0	0,21,188:7:0
+X	3849	.	T	<*>	0	.	DP=27;I16=9,17,0,0,987,37685,0,0,1395,78279,0,0,450,9368,0,0;QS=3,0;MQSB=0.282527;MQ0F=0	PL:DP:DV	0,36,255:12:0	0,21,179:7:0	0,21,190:7:0
+X	3850	.	G	<*>	0	.	DP=26;I16=9,17,0,0,957,35751,0,0,1395,78279,0,0,452,9428,0,0;QS=3,0;MQSB=0.282527;MQ0F=0	PL:DP:DV	0,36,255:12:0	0,21,179:7:0	0,21,182:7:0
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+X	3852	.	C	<*>	0	.	DP=26;I16=9,16,0,0,921,34525,0,0,1335,74679,0,0,444,9440,0,0;QS=3,0;MQSB=0.310905;MQ0F=0	PL:DP:DV	0,36,255:12:0	0,18,163:6:0	0,21,179:7:0
+X	3853	.	T	<*>	0	.	DP=28;I16=10,18,0,0,1050,40222,0,0,1484,82720,0,0,455,9641,0,0;QS=3,0;MQSB=0.515783;MQ0F=0	PL:DP:DV	0,42,255:14:0	0,21,185:7:0	0,21,192:7:0
+X	3854	.	T	<*>	0	.	DP=28;I16=10,17,0,0,955,34605,0,0,1455,81879,0,0,451,9709,0,0;QS=3,0;MQSB=0.359211;MQ0F=0	PL:DP:DV	0,45,255:15:0	0,18,171:6:0	0,18,178:6:0
+X	3855	.	C	<*>	0	.	DP=29;I16=10,18,0,0,992,36040,0,0,1515,85479,0,0,438,9264,0,0;QS=3,0;MQSB=0.331344;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,15,139:5:0	0,21,175:7:0
+X	3856	.	T	<*>	0	.	DP=30;I16=10,18,0,0,1033,38725,0,0,1546,88238,0,0,464,9982,0,0;QS=3,0;MQSB=0.190183;MQ0F=0	PL:DP:DV	0,45,255:15:0	0,18,163:6:0	0,21,185:7:0
+X	3857	.	C	<*>	0	.	DP=30;I16=10,19,0,0,1077,40979,0,0,1575,89079,0,0,447,9505,0,0;QS=3,0;MQSB=0.306875;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,15,154:5:0	0,24,194:8:0
+X	3858	.	T	<*>	0	.	DP=31;I16=10,21,0,0,1141,42567,0,0,1695,96279,0,0,477,10255,0,0;QS=3,0;MQSB=0.266219;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,18,171:6:0	0,24,208:8:0
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+X	3868	.	T	<*>	0	.	DP=33;I16=11,22,0,0,1255,48141,0,0,1792,101248,0,0,590,12494,0,0;QS=3,0;MQSB=0.161533;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,21,202:7:0	0,27,221:9:0
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+X	3870	.	T	<*>	0	.	DP=34;I16=11,23,0,0,1262,47808,0,0,1852,104848,0,0,608,12932,0,0;QS=3,0;MQSB=0.149071;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,24,215:8:0	0,27,211:9:0
+X	3871	.	T	<*>	0	.	DP=36;I16=11,25,0,0,1341,50655,0,0,1972,112048,0,0,617,13157,0,0;QS=3,0;MQSB=0.128391;MQ0F=0	PL:DP:DV	0,57,255:19:0	0,24,221:8:0	0,27,223:9:0
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+X	3873	.	T	<*>	0	.	DP=35;I16=10,24,0,0,1242,46680,0,0,1852,104848,0,0,626,13428,0,0;QS=3,0;MQSB=0.0982034;MQ0F=0	PL:DP:DV	0,57,255:19:0	0,21,194:7:0	0,24,212:8:0
+X	3874	.	T	<*>	0	.	DP=36;I16=12,24,0,0,1290,47660,0,0,1972,112048,0,0,646,13774,0,0;QS=3,0;MQSB=0.182088;MQ0F=0	PL:DP:DV	0,60,255:20:0	0,24,228:8:0	0,24,204:8:0
+X	3875	.	T	<*>	0	.	DP=37;I16=13,24,0,0,1324,48418,0,0,2029,115297,0,0,657,14061,0,0;QS=3,0;MQSB=0.117872;MQ0F=0	PL:DP:DV	0,63,255:21:0	0,24,231:8:0	0,24,197:8:0
+X	3876	.	C	<*>	0	.	DP=37;I16=13,22,0,0,1248,45354,0,0,1909,108097,0,0,623,13325,0,0;QS=3,0;MQSB=0.140806;MQ0F=0	PL:DP:DV	0,60,255:20:0	0,21,196:7:0	0,24,180:8:0
+X	3877	.	C	<*>	0	.	DP=37;I16=13,24,0,0,1363,51201,0,0,2029,115297,0,0,681,14765,0,0;QS=3,0;MQSB=0.117872;MQ0F=0	PL:DP:DV	0,63,255:21:0	0,24,217:8:0	0,24,196:8:0
+X	3878	.	A	<*>	0	.	DP=37;I16=13,23,0,0,1309,48045,0,0,1969,111697,0,0,670,14654,0,0;QS=3,0;MQSB=0.128568;MQ0F=0	PL:DP:DV	0,60,255:20:0	0,24,218:8:0	0,24,188:8:0
+X	3879	.	A	<*>	0	.	DP=38;I16=14,24,0,0,1453,56567,0,0,2066,116666,0,0,703,15543,0,0;QS=3,0;MQSB=0.076112;MQ0F=0	PL:DP:DV	0,66,255:22:0	0,24,226:8:0	0,24,206:8:0
+X	3880	.	G	<*>	0	.	DP=37;I16=14,22,0,0,1311,48735,0,0,1946,109466,0,0,689,15267,0,0;QS=3,0;MQSB=0.094094;MQ0F=0	PL:DP:DV	0,60,255:20:0	0,24,209:8:0	0,24,183:8:0
+X	3881	.	G	<*>	0	.	DP=37;I16=14,21,0,0,1200,42778,0,0,1886,105866,0,0,690,15578,0,0;QS=3,0;MQSB=0.105399;MQ0F=0	PL:DP:DV	0,63,255:21:0	0,18,178:6:0	0,24,174:8:0
+X	3882	.	T	<*>	0	.	DP=37;I16=14,21,0,0,1192,42352,0,0,1886,105866,0,0,684,15348,0,0;QS=3,0;MQSB=0.105399;MQ0F=0	PL:DP:DV	0,63,255:21:0	0,21,189:7:0	0,21,178:7:0
+X	3883	.	C	<*>	0	.	DP=38;I16=15,22,0,0,1295,46659,0,0,2006,113066,0,0,717,16279,0,0;QS=3,0;MQSB=0.124405;MQ0F=0	PL:DP:DV	0,63,255:21:0	0,24,205:8:0	0,24,171:8:0
+X	3884	.	C	<*>	0	.	DP=39;I16=16,23,0,0,1363,49387,0,0,2103,118035,0,0,749,17141,0,0;QS=3,0;MQSB=0.0760633;MQ0F=0	PL:DP:DV	0,66,255:22:0	0,24,202:8:0	0,27,212:9:0
+X	3885	.	T	<*>	0	.	DP=40;I16=16,24,0,0,1445,53663,0,0,2163,121635,0,0,754,17262,0,0;QS=3,0;MQSB=0.0679472;MQ0F=0	PL:DP:DV	0,69,255:23:0	0,24,219:8:0	0,27,214:9:0
+X	3886	.	C	<*>	0	.	DP=39;I16=16,23,0,0,1370,49762,0,0,2103,118035,0,0,761,17421,0,0;QS=3,0;MQSB=0.0760633;MQ0F=0	PL:DP:DV	0,69,255:23:0	0,24,199:8:0	0,24,191:8:0
+X	3887	.	C	<*>	0	.	DP=39;I16=16,23,0,0,1364,49222,0,0,2103,118035,0,0,767,17567,0,0;QS=3,0;MQSB=0.0760633;MQ0F=0	PL:DP:DV	0,69,255:23:0	0,24,194:8:0	0,24,201:8:0
+X	3888	.	C	<*>	0	.	DP=39;I16=15,23,0,0,1387,51885,0,0,2043,114435,0,0,747,17073,0,0;QS=3,0;MQSB=0.0555905;MQ0F=0	PL:DP:DV	0,66,255:22:0	0,24,195:8:0	0,24,208:8:0
+X	3889	.	A	<*>	0	.	DP=38;I16=15,23,0,0,1364,49918,0,0,2066,116666,0,0,777,17811,0,0;QS=3,0;MQSB=0.112471;MQ0F=0	PL:DP:DV	0,66,255:22:0	0,24,202:8:0	0,24,218:8:0
+X	3890	.	C	<*>	0	.	DP=38;I16=14,23,0,0,1362,51064,0,0,2006,113066,0,0,757,17329,0,0;QS=3,0;MQSB=0.0844255;MQ0F=0	PL:DP:DV	0,63,255:21:0	0,24,203:8:0	0,24,216:8:0
+X	3891	.	A	<*>	0	.	DP=39;I16=15,24,0,0,1466,56312,0,0,2126,120266,0,0,786,18076,0,0;QS=3,0;MQSB=0.102114;MQ0F=0	PL:DP:DV	0,66,255:22:0	0,24,203:8:0	0,27,239:9:0
+X	3892	.	G	<*>	0	.	DP=38;I16=15,23,0,0,1340,48838,0,0,2066,116666,0,0,792,18226,0,0;QS=3,0;MQSB=0.112471;MQ0F=0	PL:DP:DV	0,63,255:21:0	0,24,186:8:0	0,27,208:9:0
+X	3893	.	T	<*>	0	.	DP=39;I16=15,24,0,0,1348,48170,0,0,2126,120266,0,0,798,18404,0,0;QS=3,0;MQSB=0.102114;MQ0F=0	PL:DP:DV	0,66,255:22:0	0,24,196:8:0	0,27,212:9:0
+X	3894	.	G	<*>	0	.	DP=39;I16=15,23,0,0,1364,49900,0,0,2066,116666,0,0,779,17937,0,0;QS=3,0;MQSB=0.112471;MQ0F=0	PL:DP:DV	0,63,255:21:0	0,24,202:8:0	0,27,208:9:0
+X	3895	.	T	<*>	0	.	DP=39;I16=15,24,0,0,1375,49773,0,0,2126,120266,0,0,810,18752,0,0;QS=3,0;MQSB=0.102114;MQ0F=0	PL:DP:DV	0,66,255:22:0	0,24,202:8:0	0,27,225:9:0
+X	3896	.	A	<*>	0	.	DP=40;I16=15,24,0,0,1468,57326,0,0,2126,120266,0,0,815,18923,0,0;QS=3,0;MQSB=0.102114;MQ0F=0	PL:DP:DV	0,66,255:22:0	0,24,224:8:0	0,27,233:9:0
+X	3897	.	G	<*>	0	.	DP=40;I16=15,24,0,0,1468,56812,0,0,2126,120266,0,0,819,19021,0,0;QS=3,0;MQSB=0.102114;MQ0F=0	PL:DP:DV	0,66,255:22:0	0,21,199:7:0	0,30,234:10:0
+X	3898	.	C	<*>	0	.	DP=40;I16=15,23,0,0,1487,59351,0,0,2066,116666,0,0,813,19023,0,0;QS=3,0;MQSB=0.112471;MQ0F=0	PL:DP:DV	0,66,255:22:0	0,18,186:6:0	0,30,238:10:0
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+X	3900	.	T	<*>	0	.	DP=40;I16=15,24,0,0,1458,55516,0,0,2126,120266,0,0,833,19417,0,0;QS=3,0;MQSB=0.102114;MQ0F=0	PL:DP:DV	0,66,255:22:0	0,21,197:7:0	0,30,240:10:0
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+X	3905	.	C	<*>	0	.	DP=42;I16=15,25,0,0,1572,63314,0,0,2146,120666,0,0,822,19192,0,0;QS=3,0;MQSB=0.0381122;MQ0F=0	PL:DP:DV	0,63,255:21:0	0,24,212:8:0	0,33,255:11:0
+X	3906	.	T	<*>	0	.	DP=42;I16=16,25,0,0,1593,63039,0,0,2206,124266,0,0,846,19758,0,0;QS=3,0;MQSB=0.0536599;MQ0F=0	PL:DP:DV	0,66,255:22:0	0,24,210:8:0	0,33,253:11:0
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+X	3909	.	T	<*>	0	.	DP=43;I16=16,25,0,0,1491,55895,0,0,2201,123691,0,0,835,19697,0,0;QS=3,0;MQSB=0.0757469;MQ0F=0	PL:DP:DV	0,69,255:23:0	0,24,202:8:0	0,30,237:10:0
+X	3910	.	A	<*>	0	.	DP=40;I16=16,23,0,0,1432,53926,0,0,2081,116491,0,0,844,19724,0,0;QS=3,0;MQSB=0.0949554;MQ0F=0	PL:DP:DV	0,66,255:22:0	0,21,193:7:0	0,30,224:10:0
+X	3911	.	C	<*>	0	.	DP=40;I16=16,23,0,0,1440,55290,0,0,2081,116491,0,0,843,19613,0,0;QS=3,0;MQSB=0.0949554;MQ0F=0	PL:DP:DV	0,66,255:22:0	0,21,184:7:0	0,30,214:10:0
+X	3912	.	A	C,<*>	0	.	DP=41;I16=17,22,0,1,1358,49508,16,256,2081,116491,60,3600,830,19358,11,121;QS=2.95181,0.0481928,0;SGB=-0.556633;RPB=1;MQB=1;MQSB=0.125266;BQB=1;MQ0F=0	PL:DP:DV	0,69,255,69,255,255:23:0	0,21,166,21,166,166:7:0	0,14,202,27,205,208:10:1
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+X	3914	.	T	<*>	0	.	DP=42;I16=16,24,0,0,1512,59342,0,0,2141,120091,0,0,823,19007,0,0;QS=3,0;MQSB=0.0846181;MQ0F=0	PL:DP:DV	0,69,255:23:0	0,21,192:7:0	0,30,228:10:0
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+X	3917	.	T	<*>	0	.	DP=43;I16=16,25,0,0,1601,65219,0,0,2201,123691,0,0,825,18875,0,0;QS=3,0;MQSB=0.0757469;MQ0F=0	PL:DP:DV	0,72,255:24:0	0,21,191:7:0	0,30,254:10:0
+X	3918	.	T	<*>	0	.	DP=43;I16=16,25,0,0,1541,60711,0,0,2201,123691,0,0,801,18239,0,0;QS=3,0;MQSB=0.0757469;MQ0F=0	PL:DP:DV	0,75,255:25:0	0,18,179:6:0	0,30,254:10:0
+X	3919	.	C	<*>	0	.	DP=42;I16=15,26,0,0,1621,66337,0,0,2232,126450,0,0,826,18786,0,0;QS=3,0;MQSB=0.110793;MQ0F=0	PL:DP:DV	0,72,255:24:0	0,21,200:7:0	0,30,242:10:0
+X	3920	.	T	<*>	0	.	DP=42;I16=15,26,0,0,1605,64327,0,0,2232,126450,0,0,825,18691,0,0;QS=3,0;MQSB=0.110793;MQ0F=0	PL:DP:DV	0,72,255:24:0	0,21,207:7:0	0,30,251:10:0
+X	3921	.	T	<*>	0	.	DP=42;I16=15,26,0,0,1519,58507,0,0,2232,126450,0,0,824,18630,0,0;QS=3,0;MQSB=0.110793;MQ0F=0	PL:DP:DV	0,72,255:24:0	0,21,201:7:0	0,30,242:10:0
+X	3922	.	A	<*>	0	.	DP=42;I16=14,26,0,0,1539,61289,0,0,2195,125081,0,0,819,18545,0,0;QS=3,0;MQSB=0.168991;MQ0F=0	PL:DP:DV	0,72,255:24:0	0,18,179:6:0	0,30,244:10:0
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+X	3933	.	T	<*>	0	.	DP=38;I16=12,24,0,0,1389,54743,0,0,1958,111032,0,0,752,17366,0,0;QS=3,0;MQSB=0.218161;MQ0F=0	PL:DP:DV	0,66,255:22:0	0,18,166:6:0	0,24,220:8:0
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+X	3942	.	C	<*>	0	.	DP=35;I16=11,23,0,0,1336,54166,0,0,1892,108822,0,0,690,15772,0,0;QS=3,0;MQSB=0.231054;MQ0F=0	PL:DP:DV	0,63,255:21:0	0,15,140:5:0	0,24,195:8:0
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+X	3945	.	C	<*>	0	.	DP=33;I16=10,22,0,0,1256,51226,0,0,1772,101622,0,0,649,14657,0,0;QS=3,0;MQSB=0.187579;MQ0F=0	PL:DP:DV	0,60,255:20:0	0,15,142:5:0	0,21,177:7:0
+X	3946	.	T	<*>	0	.	DP=33;I16=10,21,0,0,1170,45884,0,0,1712,98022,0,0,609,13599,0,0;QS=3,0;MQSB=0.199344;MQ0F=0	PL:DP:DV	0,60,255:20:0	0,15,144:5:0	0,18,158:6:0
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+X	3970	.	T	<*>	0	.	DP=24;I16=11,13,0,0,861,31313,0,0,1369,80043,0,0,405,8649,0,0;QS=3,0;MQSB=0.702671;MQ0F=0	PL:DP:DV	0,54,255:18:0	0,9,83:3:0	0,9,104:3:0
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+X	3978	.	C	<*>	0	.	DP=23;I16=11,12,0,0,769,26631,0,0,1309,76443,0,0,377,8223,0,0;QS=3,0;MQSB=0.726094;MQ0F=0	PL:DP:DV	0,54,255:18:0	0,6,47:2:0	0,9,103:3:0
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+X	3980	.	T	<*>	0	.	DP=21;I16=10,11,0,0,756,27872,0,0,1212,71474,0,0,367,7855,0,0;QS=3,0;MQSB=0.914611;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,6,51:2:0	0,9,98:3:0
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+X	4063	.	C	<*>	0	.	DP=6;I16=4,2,0,0,216,7984,0,0,314,17138,0,0,102,2098,0,0;QS=1,0;MQSB=0.5;MQ0F=0	PL:DP:DV	0,18,170:6:0	0,0,0:0:0	0,0,0:0:0
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+X	4075	.	T	<*>	0	.	DP=5;I16=3,2,0,0,187,7069,0,0,254,13538,0,0,52,870,0,0;QS=1,0;MQSB=0.333333;MQ0F=0	PL:DP:DV	0,15,155:5:0	0,0,0:0:0	0,0,0:0:0
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+X	4078	.	T	<*>	0	.	DP=4;I16=3,1,0,0,143,5173,0,0,194,9938,0,0,40,644,0,0;QS=1,0;MQSB=1;MQ0F=0	PL:DP:DV	0,12,124:4:0	0,0,0:0:0	0,0,0:0:0
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+X	4080	.	T	<*>	0	.	DP=4;I16=3,0,0,0,106,3778,0,0,134,6338,0,0,25,451,0,0;QS=1,0;MQ0F=0	PL:DP:DV	0,9,87:3:0	0,0,0:0:0	0,0,0:0:0
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+X	4087	.	C	<*>	0	.	DP=2;I16=1,1,0,0,69,2405,0,0,97,4969,0,0,14,196,0,0;QS=1,0;MQSB=1;MQ0F=0	PL:DP:DV	0,6,68:2:0	0,0,0:0:0	0,0,0:0:0
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+X	4089	.	C	<*>	0	.	DP=1;I16=1,0,0,0,36,1296,0,0,37,1369,0,0,12,144,0,0;QS=1,0;MQ0F=0	PL:DP:DV	0,3,36:1:0	0,0,0:0:0	0,0,0:0:0
+X	4090	.	C	<*>	0	.	DP=1;I16=1,0,0,0,33,1089,0,0,37,1369,0,0,11,121,0,0;QS=1,0;MQ0F=0	PL:DP:DV	0,3,33:1:0	0,0,0:0:0	0,0,0:0:0
+X	4091	.	T	<*>	0	.	DP=1;I16=1,0,0,0,36,1296,0,0,37,1369,0,0,10,100,0,0;QS=1,0;MQ0F=0	PL:DP:DV	0,3,36:1:0	0,0,0:0:0	0,0,0:0:0
+X	4092	.	G	<*>	0	.	DP=1;I16=1,0,0,0,37,1369,0,0,37,1369,0,0,9,81,0,0;QS=1,0;MQ0F=0	PL:DP:DV	0,3,37:1:0	0,0,0:0:0	0,0,0:0:0
+X	4093	.	C	<*>	0	.	DP=1;I16=1,0,0,0,35,1225,0,0,37,1369,0,0,8,64,0,0;QS=1,0;MQ0F=0	PL:DP:DV	0,3,35:1:0	0,0,0:0:0	0,0,0:0:0
+X	4094	.	T	<*>	0	.	DP=1;I16=1,0,0,0,40,1600,0,0,37,1369,0,0,7,49,0,0;QS=1,0;MQ0F=0	PL:DP:DV	0,3,37:1:0	0,0,0:0:0	0,0,0:0:0
+X	4095	.	A	<*>	0	.	DP=1;I16=1,0,0,0,35,1225,0,0,37,1369,0,0,6,36,0,0;QS=1,0;MQ0F=0	PL:DP:DV	0,3,35:1:0	0,0,0:0:0	0,0,0:0:0
+X	4096	.	C	<*>	0	.	DP=1;I16=1,0,0,0,32,1024,0,0,37,1369,0,0,5,25,0,0;QS=1,0;MQ0F=0	PL:DP:DV	0,3,32:1:0	0,0,0:0:0	0,0,0:0:0
+X	4097	.	A	<*>	0	.	DP=1;I16=1,0,0,0,35,1225,0,0,37,1369,0,0,4,16,0,0;QS=1,0;MQ0F=0	PL:DP:DV	0,3,35:1:0	0,0,0:0:0	0,0,0:0:0
+X	4098	.	C	<*>	0	.	DP=1;I16=1,0,0,0,31,961,0,0,37,1369,0,0,3,9,0,0;QS=1,0;MQ0F=0	PL:DP:DV	0,3,31:1:0	0,0,0:0:0	0,0,0:0:0
+X	4099	.	T	<*>	0	.	DP=1;I16=1,0,0,0,32,1024,0,0,37,1369,0,0,2,4,0,0;QS=1,0;MQ0F=0	PL:DP:DV	0,3,32:1:0	0,0,0:0:0	0,0,0:0:0
+X	4100	.	C	<*>	0	.	DP=1;I16=1,0,0,0,27,729,0,0,37,1369,0,0,1,1,0,0;QS=1,0;MQ0F=0	PL:DP:DV	0,3,27:1:0	0,0,0:0:0	0,0,0:0:0
+X	4101	.	C	<*>	0	.	DP=1;I16=1,0,0,0,26,676,0,0,37,1369,0,0,0,0,0,0;QS=1,0;MQ0F=0	PL:DP:DV	0,3,26:1:0	0,0,0:0:0	0,0,0:0:0
diff --git a/test/mpileup.c.1.out b/test/mpileup.c.1.out
new file mode 100644
index 0000000..1c4a0c8
--- /dev/null
+++ b/test/mpileup.c.1.out
@@ -0,0 +1,43 @@
+##fileformat=VCFv4.2
+##FILTER=<ID=PASS,Description="All filters passed">
+##samtoolsVersion=1.1-19-g6b249e2+htslib-1.1-74-g845c515
+##samtoolsCommand=samtools mpileup -uvDV -b xxx//mpileup.bam.list -f xxx//mpileup.ref.fa.gz
+##reference=file://xxx//mpileup.ref.fa.gz
+##contig=<ID=17,length=81195210>
+##ALT=<ID=X,Description="Represents allele(s) other than observed.">
+##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
+##INFO=<ID=IDV,Number=1,Type=Integer,Description="Maximum number of reads supporting an indel">
+##INFO=<ID=IMF,Number=1,Type=Float,Description="Maximum fraction of reads supporting an indel">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">
+##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias for filtering splice-site artefacts in RNA-seq data (bigger is better)",Version="3">
+##INFO=<ID=RPB,Number=1,Type=Float,Description="Mann-Whitney U test of Read Position Bias (bigger is better)">
+##INFO=<ID=MQB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality Bias (bigger is better)">
+##INFO=<ID=BQB,Number=1,Type=Float,Description="Mann-Whitney U test of Base Quality Bias (bigger is better)">
+##INFO=<ID=MQSB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality vs Strand Bias (bigger is better)">
+##INFO=<ID=SGB,Number=1,Type=Float,Description="Segregation based metric.">
+##INFO=<ID=MQ0F,Number=1,Type=Float,Description="Fraction of MQ0 reads (smaller is better)">
+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Number of high-quality bases">
+##FORMAT=<ID=DV,Number=1,Type=Integer,Description="Number of high-quality non-reference bases">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##INFO=<ID=AF1,Number=1,Type=Float,Description="Max-likelihood estimate of the first ALT allele frequency (assuming HWE)">
+##INFO=<ID=AF2,Number=1,Type=Float,Description="Max-likelihood estimate of the first and second group ALT allele frequency (assuming HWE)">
+##INFO=<ID=AC1,Number=1,Type=Float,Description="Max-likelihood estimate of the first ALT allele count (no HWE assumption)">
+##INFO=<ID=MQ,Number=1,Type=Integer,Description="Root-mean-square mapping quality of covering reads">
+##INFO=<ID=FQ,Number=1,Type=Float,Description="Phred probability of all samples being the same">
+##INFO=<ID=PV4,Number=4,Type=Float,Description="P-values for strand bias, baseQ bias, mapQ bias and tail distance bias">
+##INFO=<ID=G3,Number=3,Type=Float,Description="ML estimate of genotype frequencies">
+##INFO=<ID=HWE,Number=1,Type=Float,Description="Chi^2 based HWE test P-value based on G3">
+##INFO=<ID=DP4,Number=4,Type=Integer,Description="Number of high-quality ref-forward , ref-reverse, alt-forward and alt-reverse bases">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	HG00100	HG00101	HG00102
+17	302	.	T	TA	999	.	INDEL;IDV=7;IMF=1;DP=25;VDB=0.27613;SGB=-4.22417;MQSB=0.0443614;MQ0F=0;AF1=0.685575;AC1=4;DP4=2,4,8,11;MQ=51;FQ=61.4911;PV4=1,1,1,1	GT:PL:DP:DV	0/1:167,0,96:11:6	0/1:157,0,9:7:6	1/1:201,21,0:7:7
+17	828	.	T	C	999	.	DP=25;VDB=0.842082;SGB=-4.20907;RPB=0.950652;MQB=1;MQSB=1;BQB=0.929717;MQ0F=0;AF1=0.656389;AC1=4;DP4=2,4,8,11;MQ=60;FQ=89.3748;PV4=1,1,1,0.32233	GT:PL:DP:DV	0/1:211,0,35:12:10	0/1:116,0,91:9:5	1/1:120,12,0:4:4
+17	834	.	G	A	999	.	DP=25;VDB=0.788006;SGB=-4.01214;RPB=0.999233;MQB=1;MQSB=1;BQB=0.821668;MQ0F=0;AF1=0.646503;AC1=4;DP4=2,3,7,10;MQ=60;FQ=68.6952;PV4=1,1,1,0.228905	GT:PL:DP:DV	0/1:185,0,46:11:9	0/1:128,0,59:8:5	1/1:89,9,0:3:3
+17	1665	.	T	C	3.14059	.	DP=20;VDB=0.1;SGB=0.346553;RPB=0.222222;MQB=0.611111;MQSB=0.988166;BQB=0.944444;MQ0F=0;AF1=0.167199;AC1=1;DP4=7,11,1,1;MQ=56;FQ=3.56819;PV4=1,0.239991,0.0798553,0.27333	GT:PL:DP:DV	0/0:0,21,185:7:0	0/0:0,27,222:9:0	0/1:35,0,51:4:2
+17	1869	.	A	T	134.348	.	DP=24;VDB=0.928022;SGB=-11.9537;RPB=0.984127;MQB=0.96464;MQSB=0.931547;BQB=0.359155;MQ0F=0;AF1=0.598209;AC1=4;DP4=6,9,5,4;MQ=59;FQ=138.299;PV4=0.675175,0.0234896,1,0.324361	GT:PL:DP:DV	0/1:115,0,224:18:7	0/1:16,0,104:5:1	1/1:42,3,0:1:1
+17	2041	.	G	A	999	.	DP=31;VDB=0.816435;SGB=-4.18892;RPB=0.88473;MQB=0.972375;MQSB=0.968257;BQB=0.311275;MQ0F=0;AF1=0.665982;AC1=4;DP4=6,5,12,7;MQ=59;FQ=999;PV4=0.71163,1,0.228209,0.143795	GT:PL:DP:DV	0/1:229,0,212:21:11	0/1:32,0,24:2:1	1/1:223,21,0:7:7
+17	2220	.	G	A	999	.	DP=21;VDB=0.532753;SGB=-3.51597;RPB=0.964198;MQB=0.898397;MQSB=0.875769;BQB=0.0354359;MQ0F=0;AF1=0.656341;AC1=4;DP4=6,2,1,11;MQ=59;FQ=139.373;PV4=0.00443756,1,1,1	GT:PL:DP:DV	0/1:139,0,130:12:6	0/1:69,0,46:4:2	1/1:131,12,0:4:4
+17	2564	.	A	G	227.769	.	DP=15;VDB=0.690812;SGB=-3.20711;RPB=0.197899;MQB=1;MQSB=1;BQB=0.965069;MQ0F=0;AF1=0.656337;AC1=4;DP4=1,4,4,5;MQ=60;FQ=97.3723;PV4=0.58042,1,1,1	GT:PL:DP:DV	0/1:88,0,78:6:3	0/1:57,0,56:4:2	1/1:124,12,0:4:4
+17	3104	.	C	T	24.364	.	DP=25;VDB=0.8;SGB=0.346553;RPB=0.717391;MQB=0.956522;MQSB=0.962269;BQB=0.978261;MQ0F=0;AF1=0.170892;AC1=1;DP4=8,15,2,0;MQ=59;FQ=25.179;PV4=0.15,1,1,1	GT:PL:DP:DV	0/0:0,48,255:16:0	0/0:0,12,144:4:0	0/1:59,0,93:5:2
+17	3587	.	G	A	353.302	.	DP=29;VDB=0.902044;SGB=-3.91326;RPB=0.800999;MQB=1;MQSB=1;BQB=0.156944;MQ0F=0;AF1=0.665739;AC1=4;DP4=4,7,10,6;MQ=60;FQ=358.057;PV4=0.25186,0.0986321,1,1	GT:PL:DP:DV	0/1:161,0,184:14:7	0/1:22,0,118:5:1	1/1:212,24,0:8:8
+17	3936	.	A	G	999	.	DP=37;VDB=0.0574114;SGB=-4.60123;RPB=0.741697;MQB=0.812605;MQSB=0.143788;BQB=0.883831;MQ0F=0;AF1=0.666004;AC1=4;DP4=5,6,6,17;MQ=57;FQ=999;PV4=0.434446,0.125787,1,1	GT:PL:DP:DV	0/1:233,0,206:20:11	0/1:77,0,58:6:4	1/1:196,24,0:8:8
diff --git a/test/mpileup.c.X.out b/test/mpileup.c.X.out
new file mode 100644
index 0000000..e35b12b
--- /dev/null
+++ b/test/mpileup.c.X.out
@@ -0,0 +1,43 @@
+##fileformat=VCFv4.2
+##FILTER=<ID=PASS,Description="All filters passed">
+##samtoolsVersion=1.1-19-g6b249e2+htslib-1.1-74-g845c515
+##samtoolsCommand=samtools mpileup -uvDV -b xxx//mpileup.bam.list -f xxx//mpileup.ref.fa.gz
+##reference=file://xxx//mpileup.ref.fa.gz
+##contig=<ID=X,length=81195210>
+##ALT=<ID=X,Description="Represents allele(s) other than observed.">
+##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
+##INFO=<ID=IDV,Number=1,Type=Integer,Description="Maximum number of reads supporting an indel">
+##INFO=<ID=IMF,Number=1,Type=Float,Description="Maximum fraction of reads supporting an indel">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">
+##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias for filtering splice-site artefacts in RNA-seq data (bigger is better)",Version="3">
+##INFO=<ID=RPB,Number=1,Type=Float,Description="Mann-Whitney U test of Read Position Bias (bigger is better)">
+##INFO=<ID=MQB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality Bias (bigger is better)">
+##INFO=<ID=BQB,Number=1,Type=Float,Description="Mann-Whitney U test of Base Quality Bias (bigger is better)">
+##INFO=<ID=MQSB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality vs Strand Bias (bigger is better)">
+##INFO=<ID=SGB,Number=1,Type=Float,Description="Segregation based metric.">
+##INFO=<ID=MQ0F,Number=1,Type=Float,Description="Fraction of MQ0 reads (smaller is better)">
+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Number of high-quality bases">
+##FORMAT=<ID=DV,Number=1,Type=Integer,Description="Number of high-quality non-reference bases">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##INFO=<ID=AF1,Number=1,Type=Float,Description="Max-likelihood estimate of the first ALT allele frequency (assuming HWE)">
+##INFO=<ID=AF2,Number=1,Type=Float,Description="Max-likelihood estimate of the first and second group ALT allele frequency (assuming HWE)">
+##INFO=<ID=AC1,Number=1,Type=Float,Description="Max-likelihood estimate of the first ALT allele count (no HWE assumption)">
+##INFO=<ID=MQ,Number=1,Type=Integer,Description="Root-mean-square mapping quality of covering reads">
+##INFO=<ID=FQ,Number=1,Type=Float,Description="Phred probability of all samples being the same">
+##INFO=<ID=PV4,Number=4,Type=Float,Description="P-values for strand bias, baseQ bias, mapQ bias and tail distance bias">
+##INFO=<ID=G3,Number=3,Type=Float,Description="ML estimate of genotype frequencies">
+##INFO=<ID=HWE,Number=1,Type=Float,Description="Chi^2 based HWE test P-value based on G3">
+##INFO=<ID=DP4,Number=4,Type=Integer,Description="Number of high-quality ref-forward , ref-reverse, alt-forward and alt-reverse bases">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	HG00100	HG00101	HG00102
+X	302	.	T	TA	999	.	INDEL;IDV=7;IMF=1;DP=25;VDB=0.27613;SGB=-4.22417;MQSB=0.0443614;MQ0F=0;AF1=0.685575;AC1=4;DP4=2,4,8,11;MQ=51;FQ=61.4911;PV4=1,1,1,1	GT:PL:DP:DV	0/1:167,0,96:11:6	0:157,0,9:7:6	1/1:201,21,0:7:7
+X	828	.	T	C	999	.	DP=25;VDB=0.842082;SGB=-4.20907;RPB=0.950652;MQB=1;MQSB=1;BQB=0.929717;MQ0F=0;AF1=0.656389;AC1=4;DP4=2,4,8,11;MQ=60;FQ=89.3748;PV4=1,1,1,0.32233	GT:PL:DP:DV	0/1:211,0,35:12:10	0:116,91:9:5	1/1:120,12,0:4:4
+X	834	.	G	A	999	.	DP=25;VDB=0.788006;SGB=-4.01214;RPB=0.999233;MQB=1;MQSB=1;BQB=0.821668;MQ0F=0;AF1=0.646503;AC1=4;DP4=2,3,7,10;MQ=60;FQ=68.6952;PV4=1,1,1,0.228905	GT:PL:DP:DV	0/1:185,0,46:11:9	0:128,59:8:5	1/1:89,9,0:3:3
+X	1665	.	T	C	3.14059	.	DP=20;VDB=0.1;SGB=0.346553;RPB=0.222222;MQB=0.611111;MQSB=0.988166;BQB=0.944444;MQ0F=0;AF1=0.167199;AC1=1;DP4=7,11,1,1;MQ=56;FQ=3.56819;PV4=1,0.239991,0.0798553,0.27333	GT:PL:DP:DV	0/0:0,21,185:7:0	0/0:0,27,222:9:0	0/1:35,0,51:4:2
+X	1869	.	A	T	134.348	.	DP=24;VDB=0.928022;SGB=-11.9537;RPB=0.984127;MQB=0.96464;MQSB=0.931547;BQB=0.359155;MQ0F=0;AF1=0.598209;AC1=4;DP4=6,9,5,4;MQ=59;FQ=138.299;PV4=0.675175,0.0234896,1,0.324361	GT:PL:DP:DV	0/1:115,0,224:18:7	0/1:16,0,104:5:1	1/1:42,3,0:1:1
+X	2041	.	G	A	999	.	DP=31;VDB=0.816435;SGB=-4.18892;RPB=0.88473;MQB=0.972375;MQSB=0.968257;BQB=0.311275;MQ0F=0;AF1=0.665982;AC1=4;DP4=6,5,12,7;MQ=59;FQ=999;PV4=0.71163,1,0.228209,0.143795	GT:PL:DP:DV	0/1:229,0,212:21:11	0/1:32,0,24:2:1	1/1:223,21,0:7:7
+X	2220	.	G	A	999	.	DP=21;VDB=0.532753;SGB=-3.51597;RPB=0.964198;MQB=0.898397;MQSB=0.875769;BQB=0.0354359;MQ0F=0;AF1=0.656341;AC1=4;DP4=6,2,1,11;MQ=59;FQ=139.373;PV4=0.00443756,1,1,1	GT:PL:DP:DV	0/1:139,0,130:12:6	0/1:69,0,46:4:2	1/1:131,12,0:4:4
+X	2564	.	A	G	227.769	.	DP=15;VDB=0.690812;SGB=-3.20711;RPB=0.197899;MQB=1;MQSB=1;BQB=0.965069;MQ0F=0;AF1=0.656337;AC1=4;DP4=1,4,4,5;MQ=60;FQ=97.3723;PV4=0.58042,1,1,1	GT:PL:DP:DV	0/1:88,0,78:6:3	0/1:57,0,56:4:2	1/1:124,12,0:4:4
+X	3104	.	C	T	24.364	.	DP=25;VDB=0.8;SGB=0.346553;RPB=0.717391;MQB=0.956522;MQSB=0.962269;BQB=0.978261;MQ0F=0;AF1=0.170892;AC1=1;DP4=8,15,2,0;MQ=59;FQ=25.179;PV4=0.15,1,1,1	GT:PL:DP:DV	0/0:0,48,255:16:0	0:0,144:4:0	0/1:59,0,93:5:2
+X	3587	.	G	A	353.302	.	DP=29;VDB=0.902044;SGB=-3.91326;RPB=0.800999;MQB=1;MQSB=1;BQB=0.156944;MQ0F=0;AF1=0.665739;AC1=4;DP4=4,7,10,6;MQ=60;FQ=358.057;PV4=0.25186,0.0986321,1,1	GT:PL:DP:DV	0/1:161,0,184:14:7	0:22,118:5:1	1/1:212,24,0:8:8
+X	3936	.	A	G	999	.	DP=37;VDB=0.0574114;SGB=-4.60123;RPB=0.741697;MQB=0.812605;MQSB=0.143788;BQB=0.883831;MQ0F=0;AF1=0.666004;AC1=4;DP4=5,6,6,17;MQ=57;FQ=999;PV4=0.434446,0.125787,1,1	GT:PL:DP:DV	0/1:233,0,206:20:11	0:77,58:6:4	1/1:196,24,0:8:8
diff --git a/test/mpileup.c.X.vcf b/test/mpileup.c.X.vcf
new file mode 100644
index 0000000..ea2983a
--- /dev/null
+++ b/test/mpileup.c.X.vcf
@@ -0,0 +1,4127 @@
+##fileformat=VCFv4.2
+##FILTER=<ID=PASS,Description="All filters passed">
+##samtoolsVersion=1.1-19-g6b249e2+htslib-1.1-74-g845c515
+##samtoolsCommand=samtools mpileup -uvDV -b xxx//mpileup.bam.list -f xxx//mpileup.ref.fa.gz
+##reference=file://xxx//mpileup.ref.fa.gz
+##contig=<ID=X,length=81195210>
+##ALT=<ID=X,Description="Represents allele(s) other than observed.">
+##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
+##INFO=<ID=IDV,Number=1,Type=Integer,Description="Maximum number of reads supporting an indel">
+##INFO=<ID=IMF,Number=1,Type=Float,Description="Maximum fraction of reads supporting an indel">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">
+##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias for filtering splice-site artefacts in RNA-seq data (bigger is better)",Version="3">
+##INFO=<ID=RPB,Number=1,Type=Float,Description="Mann-Whitney U test of Read Position Bias (bigger is better)">
+##INFO=<ID=MQB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality Bias (bigger is better)">
+##INFO=<ID=BQB,Number=1,Type=Float,Description="Mann-Whitney U test of Base Quality Bias (bigger is better)">
+##INFO=<ID=MQSB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality vs Strand Bias (bigger is better)">
+##INFO=<ID=SGB,Number=1,Type=Float,Description="Segregation based metric.">
+##INFO=<ID=MQ0F,Number=1,Type=Float,Description="Fraction of MQ0 reads (smaller is better)">
+##INFO=<ID=I16,Number=16,Type=Float,Description="Auxiliary tag used for calling, see description of bcf_callret1_t in bam2bcf.h">
+##INFO=<ID=QS,Number=R,Type=Float,Description="Auxiliary tag used for calling">
+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Number of high-quality bases">
+##FORMAT=<ID=DV,Number=1,Type=Integer,Description="Number of high-quality non-reference bases">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	HG00100	HG00101	HG00102
+X	1	.	A	<*>	0	.	DP=11;I16=11,0,0,0,452,18594,0,0,319,9251,0,0,223,4959,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,72:3:0
+X	2	.	A	<*>	0	.	DP=11;I16=11,0,0,0,439,17587,0,0,319,9251,0,0,226,5030,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,72:3:0
+X	3	.	G	<*>	0	.	DP=11;I16=11,0,0,0,431,16971,0,0,319,9251,0,0,229,5111,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,72:3:0
+X	4	.	C	<*>	0	.	DP=11;I16=11,0,0,0,423,16417,0,0,319,9251,0,0,232,5202,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,71:3:0
+X	5	.	T	<*>	0	.	DP=11;I16=11,0,0,0,450,18520,0,0,319,9251,0,0,234,5252,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,72:3:0
+X	6	.	T	<*>	0	.	DP=11;I16=11,0,0,0,403,14847,0,0,319,9251,0,0,236,5310,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,72:3:0
+X	7	.	C	<*>	0	.	DP=11;I16=11,0,0,0,446,18114,0,0,319,9251,0,0,237,5327,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,72:3:0
+X	8	.	T	<*>	0	.	DP=11;I16=11,0,0,0,465,19677,0,0,319,9251,0,0,238,5354,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,72:3:0
+X	9	.	C	<*>	0	.	DP=11;I16=11,0,0,0,447,18205,0,0,319,9251,0,0,239,5391,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,72:3:0
+X	10	.	A	<*>	0	.	DP=11;I16=11,0,0,0,426,16756,0,0,319,9251,0,0,240,5438,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,69:3:0
+X	11	.	C	<*>	0	.	DP=11;I16=11,0,0,0,413,15603,0,0,319,9251,0,0,241,5495,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,72:3:0
+X	12	.	C	<*>	0	.	DP=11;I16=11,0,0,0,438,17506,0,0,319,9251,0,0,242,5562,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,72:3:0
+X	13	.	C	<*>	0	.	DP=11;I16=11,0,0,0,437,17463,0,0,319,9251,0,0,243,5639,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,72:3:0
+X	14	.	T	<*>	0	.	DP=11;I16=11,0,0,0,453,18715,0,0,319,9251,0,0,242,5628,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,72:3:0
+X	15	.	G	<*>	0	.	DP=11;I16=11,0,0,0,439,17599,0,0,319,9251,0,0,240,5580,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,72:3:0
+X	16	.	T	<*>	0	.	DP=11;I16=11,0,0,0,426,16546,0,0,319,9251,0,0,238,5544,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,72:3:0
+X	17	.	T	<*>	0	.	DP=11;I16=11,0,0,0,407,15195,0,0,319,9251,0,0,235,5469,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,72:3:0
+X	18	.	C	<*>	0	.	DP=12;I16=12,0,0,0,450,17136,0,0,379,12851,0,0,231,5353,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,18,113:6:0	0,9,72:3:0	0,9,72:3:0
+X	19	.	C	<*>	0	.	DP=13;I16=13,0,0,0,502,19652,0,0,439,16451,0,0,228,5246,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,18,112:6:0	0,12,89:4:0	0,9,72:3:0
+X	20	.	T	<*>	0	.	DP=13;I16=13,0,0,0,532,21878,0,0,439,16451,0,0,226,5150,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,18,116:6:0	0,12,98:4:0	0,9,72:3:0
+X	21	.	G	<*>	0	.	DP=13;I16=13,0,0,0,498,19254,0,0,439,16451,0,0,224,5066,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,18,117:6:0	0,12,94:4:0	0,9,72:3:0
+X	22	.	C	<*>	0	.	DP=13;I16=13,0,0,0,511,20289,0,0,470,19210,0,0,223,4993,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,18,115:6:0	0,12,91:4:0	0,9,76:3:0
+X	23	.	A	<*>	0	.	DP=14;I16=14,0,0,0,513,19399,0,0,530,22810,0,0,223,4931,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,21,133:7:0	0,12,82:4:0	0,9,82:3:0
+X	24	.	T	<*>	0	.	DP=14;I16=14,0,0,0,534,20540,0,0,530,22810,0,0,224,4882,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,21,131:7:0	0,12,96:4:0	0,9,80:3:0
+X	25	.	A	<*>	0	.	DP=15;I16=15,0,0,0,561,21133,0,0,590,26410,0,0,225,4847,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,24,140:8:0	0,12,96:4:0	0,9,81:3:0
+X	26	.	G	<*>	0	.	DP=15;I16=15,0,0,0,591,23429,0,0,590,26410,0,0,227,4827,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,24,151:8:0	0,12,96:4:0	0,9,81:3:0
+X	27	.	A	<*>	0	.	DP=15;I16=15,0,0,0,588,23120,0,0,590,26410,0,0,229,4823,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,24,146:8:0	0,12,98:4:0	0,9,83:3:0
+X	28	.	T	<*>	0	.	DP=16;I16=16,0,0,0,605,23001,0,0,650,30010,0,0,231,4835,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,24,147:8:0	0,12,97:4:0	0,12,101:4:0
+X	29	.	A	<*>	0	.	DP=17;I16=17,0,0,0,615,22533,0,0,710,33610,0,0,234,4864,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,24,146:8:0	0,15,102:5:0	0,12,104:4:0
+X	30	.	A	<*>	0	.	DP=17;I16=17,0,0,0,660,25914,0,0,710,33610,0,0,238,4912,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,24,149:8:0	0,15,115:5:0	0,12,108:4:0
+X	31	.	T	<*>	0	.	DP=17;I16=17,0,0,0,656,25392,0,0,710,33610,0,0,242,4980,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,24,150:8:0	0,15,113:5:0	0,12,105:4:0
+X	32	.	T	<*>	0	.	DP=17;I16=17,0,0,0,605,21789,0,0,741,36369,0,0,247,5067,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,24,143:8:0	0,15,104:5:0	0,12,104:4:0
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+X	1914	.	C	<*>	0	.	DP=27;I16=15,12,0,0,1010,38762,0,0,1577,93889,0,0,561,12703,0,0;QS=3,0;MQSB=0.958048;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,24,221:8:0	0,6,75:2:0
+X	1915	.	T	C,<*>	0	.	DP=27;I16=14,12,1,0,974,37184,16,256,1560,93600,17,289,543,12389,18,324;QS=2.97351,0.0264901,0;SGB=-0.556633;RPB=1;MQB=1;MQSB=0.958048;BQB=1;MQ0F=0	PL:DP:DV	0,34,255,48,255,255:17:1	0,24,231,24,231,231:8:0	0,6,60,6,60,60:2:0
+X	1916	.	G	T,<*>	0	.	DP=27;I16=14,12,1,0,991,38291,15,225,1560,93600,17,289,544,12454,17,289;QS=2.97581,0.0241935,0;SGB=-0.556633;RPB=1;MQB=1;MQSB=0.958048;BQB=1;MQ0F=0	PL:DP:DV	0,35,255,48,255,255:17:1	0,24,226,24,226,226:8:0	0,6,69,6,69,69:2:0
+X	1917	.	C	<*>	0	.	DP=27;I16=15,12,0,0,1030,39740,0,0,1577,93889,0,0,561,12793,0,0;QS=3,0;MQSB=0.958048;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,24,214:8:0	0,6,73:2:0
+X	1918	.	A	<*>	0	.	DP=27;I16=15,11,0,0,963,36201,0,0,1517,90289,0,0,542,12502,0,0;QS=3,0;MQSB=0.960078;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,24,217:8:0	0,6,72:2:0
+X	1919	.	C	<*>	0	.	DP=27;I16=15,12,0,0,987,36651,0,0,1577,93889,0,0,560,12902,0,0;QS=3,0;MQSB=0.958048;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,24,214:8:0	0,6,72:2:0
+X	1920	.	A	T,<*>	0	.	DP=29;I16=15,12,0,1,1007,38337,14,196,1546,91130,60,3600,538,12518,21,441;QS=2.97647,0.0235294,0;SGB=-0.556633;RPB=1;MQB=1;MQSB=0.999735;BQB=1;MQ0F=0	PL:DP:DV	0,36,255,48,255,255:17:1	0,24,225,24,225,225:8:0	0,9,101,9,101,101:3:0
+X	1921	.	G	<*>	0	.	DP=30;I16=15,14,0,0,1059,39815,0,0,1666,98330,0,0,542,12474,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,54,255:18:0	0,21,182:7:0	0,12,132:4:0
+X	1922	.	T	<*>	0	.	DP=29;I16=14,14,0,0,1013,37513,0,0,1649,98041,0,0,532,12418,0,0;QS=3,0;MQSB=0.949591;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,21,197:7:0	0,12,134:4:0
+X	1923	.	G	<*>	0	.	DP=28;I16=14,14,0,0,1034,38974,0,0,1606,94730,0,0,545,12629,0,0;QS=3,0;MQSB=0.999736;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,21,188:7:0	0,12,126:4:0
+X	1924	.	C	<*>	0	.	DP=27;I16=13,13,0,0,965,36587,0,0,1486,87530,0,0,521,12017,0,0;QS=3,0;MQSB=0.999671;MQ0F=0	PL:DP:DV	0,45,255:15:0	0,21,183:7:0	0,12,116:4:0
+X	1925	.	C	<*>	0	.	DP=27;I16=14,13,0,0,987,37021,0,0,1546,91130,0,0,546,12626,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,21,187:7:0	0,12,124:4:0
+X	1926	.	T	<*>	0	.	DP=27;I16=14,13,0,0,1031,40057,0,0,1546,91130,0,0,545,12581,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,21,197:7:0	0,12,141:4:0
+X	1927	.	T	<*>	0	.	DP=27;I16=13,13,0,0,959,35773,0,0,1529,90841,0,0,538,12522,0,0;QS=3,0;MQSB=0.945959;MQ0F=0	PL:DP:DV	0,45,255:15:0	0,21,191:7:0	0,12,133:4:0
+X	1928	.	C	<*>	0	.	DP=27;I16=13,13,0,0,986,38264,0,0,1529,90841,0,0,538,12532,0,0;QS=3,0;MQSB=0.945959;MQ0F=0	PL:DP:DV	0,45,255:15:0	0,21,189:7:0	0,12,125:4:0
+X	1929	.	T	<*>	0	.	DP=27;I16=13,13,0,0,990,38630,0,0,1529,90841,0,0,538,12562,0,0;QS=3,0;MQSB=0.945959;MQ0F=0	PL:DP:DV	0,45,255:15:0	0,21,189:7:0	0,12,139:4:0
+X	1930	.	G	<*>	0	.	DP=26;I16=13,11,0,0,905,34865,0,0,1409,83641,0,0,521,12271,0,0;QS=3,0;MQSB=0.931547;MQ0F=0	PL:DP:DV	0,45,255:15:0	0,18,179:6:0	0,9,99:3:0
+X	1931	.	C	<*>	0	.	DP=27;I16=15,12,0,0,967,36293,0,0,1546,91130,0,0,540,12578,0,0;QS=3,0;MQSB=0.99881;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,18,165:6:0	0,12,121:4:0
+X	1932	.	T	<*>	0	.	DP=27;I16=14,13,0,0,998,38154,0,0,1546,91130,0,0,541,12605,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,15,143:5:0	0,15,146:5:0
+X	1933	.	T	<*>	0	.	DP=27;I16=14,13,0,0,962,35344,0,0,1546,91130,0,0,542,12602,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,15,142:5:0	0,15,158:5:0
+X	1934	.	G	<*>	0	.	DP=27;I16=13,13,0,0,987,38219,0,0,1529,90841,0,0,543,12569,0,0;QS=3,0;MQSB=0.945959;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,15,134:5:0	0,15,143:5:0
+X	1935	.	C	<*>	0	.	DP=27;I16=14,12,0,0,963,36627,0,0,1529,90841,0,0,520,11930,0,0;QS=3,0;MQSB=0.937241;MQ0F=0	PL:DP:DV	0,45,255:15:0	0,18,162:6:0	0,15,154:5:0
+X	1936	.	C	<*>	0	.	DP=27;I16=14,13,0,0,1018,39406,0,0,1589,94441,0,0,547,12561,0,0;QS=3,0;MQSB=0.94394;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,18,177:6:0	0,15,159:5:0
+X	1937	.	T	<*>	0	.	DP=27;I16=14,13,0,0,1036,40636,0,0,1589,94441,0,0,547,12489,0,0;QS=3,0;MQSB=0.94394;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,18,182:6:0	0,15,170:5:0
+X	1938	.	G	<*>	0	.	DP=27;I16=14,13,0,0,1001,38377,0,0,1589,94441,0,0,546,12392,0,0;QS=3,0;MQSB=0.94394;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,18,166:6:0	0,15,155:5:0
+X	1939	.	T	<*>	0	.	DP=27;I16=14,12,0,0,964,36430,0,0,1560,93600,0,0,525,11909,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,18,167:6:0	0,12,144:4:0
+X	1940	.	G	<*>	0	.	DP=27;I16=14,13,0,0,1003,37937,0,0,1589,94441,0,0,542,12172,0,0;QS=3,0;MQSB=0.94394;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,18,159:6:0	0,15,155:5:0
+X	1941	.	G	<*>	0	.	DP=27;I16=14,13,0,0,1004,38072,0,0,1589,94441,0,0,540,12098,0,0;QS=3,0;MQSB=0.94394;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,18,176:6:0	0,15,156:5:0
+X	1942	.	C	<*>	0	.	DP=27;I16=14,12,0,0,996,38790,0,0,1560,93600,0,0,516,11564,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,18,174:6:0	0,12,140:4:0
+X	1943	.	T	<*>	0	.	DP=27;I16=14,13,0,0,1044,40952,0,0,1589,94441,0,0,536,12022,0,0;QS=3,0;MQSB=0.94394;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,18,184:6:0	0,15,167:5:0
+X	1944	.	T	<*>	0	.	DP=27;I16=14,13,0,0,987,37237,0,0,1589,94441,0,0,533,11971,0,0;QS=3,0;MQSB=0.94394;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,18,175:6:0	0,15,170:5:0
+X	1945	.	T	<*>	0	.	DP=27;I16=14,13,0,0,993,37067,0,0,1589,94441,0,0,530,11946,0,0;QS=3,0;MQSB=0.94394;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,18,174:6:0	0,15,171:5:0
+X	1946	.	G	<*>	0	.	DP=27;I16=14,13,0,0,1013,38617,0,0,1589,94441,0,0,526,11896,0,0;QS=3,0;MQSB=0.94394;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,18,162:6:0	0,15,162:5:0
+X	1947	.	A	<*>	0	.	DP=26;I16=13,13,0,0,950,35522,0,0,1529,90841,0,0,522,11818,0,0;QS=3,0;MQSB=0.945959;MQ0F=0	PL:DP:DV	0,45,255:15:0	0,18,167:6:0	0,15,160:5:0
+X	1948	.	G	C,<*>	0	.	DP=27;I16=14,12,0,1,966,36912,16,256,1560,93600,29,841,493,11135,25,625;QS=2.90361,0.0963855,0;SGB=-0.556633;RPB=1;MQB=1;MQSB=0.94394;BQB=1;MQ0F=0	PL:DP:DV	0,45,255,45,255,255:15:0	0,21,190,21,190,190:7:0	1,0,123,13,126,132:5:1
+X	1949	.	A	<*>	0	.	DP=26;I16=14,11,0,0,871,31325,0,0,1469,87241,0,0,490,11048,0,0;QS=3,0;MQSB=0.929204;MQ0F=0	PL:DP:DV	0,39,255:13:0	0,21,174:7:0	0,15,155:5:0
+X	1950	.	A	<*>	0	.	DP=27;I16=14,13,0,0,1007,38049,0,0,1589,94441,0,0,511,11559,0,0;QS=3,0;MQSB=0.94394;MQ0F=0	PL:DP:DV	0,42,255:14:0	0,21,205:7:0	0,18,176:6:0
+X	1951	.	G	<*>	0	.	DP=27;I16=14,13,0,0,960,35536,0,0,1589,94441,0,0,509,11469,0,0;QS=3,0;MQSB=0.94394;MQ0F=0	PL:DP:DV	0,42,255:14:0	0,21,180:7:0	0,18,181:6:0
+X	1952	.	A	<*>	0	.	DP=27;I16=14,12,0,0,924,33366,0,0,1529,90841,0,0,483,10779,0,0;QS=3,0;MQSB=0.937241;MQ0F=0	PL:DP:DV	0,39,255:13:0	0,21,184:7:0	0,18,182:6:0
+X	1953	.	A	<*>	0	.	DP=28;I16=15,12,0,0,925,32719,0,0,1589,94441,0,0,482,10740,0,0;QS=3,0;MQSB=0.935229;MQ0F=0	PL:DP:DV	0,42,255:14:0	0,21,189:7:0	0,18,168:6:0
+X	1954	.	A	C,<*>	0	.	DP=29;I16=14,13,0,1,929,33219,18,324,1620,97200,29,841,475,10679,25,625;QS=2.90217,0.0978261,0;SGB=-0.556633;RPB=1;MQB=1;MQSB=0.949591;BQB=1;MQ0F=0	PL:DP:DV	0,45,255,45,255,255:15:0	0,21,198,21,198,198:7:0	0,0,130,15,133,141:6:1
+X	1955	.	C	<*>	0	.	DP=29;I16=14,12,0,0,961,36067,0,0,1560,93600,0,0,451,10035,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,42,255:14:0	0,21,206:7:0	0,15,165:5:0
+X	1956	.	C	<*>	0	.	DP=29;I16=14,13,0,0,964,35402,0,0,1620,97200,0,0,475,10573,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,45,255:15:0	0,21,196:7:0	0,15,164:5:0
+X	1957	.	C	<*>	0	.	DP=29;I16=14,13,0,0,980,36212,0,0,1620,97200,0,0,472,10420,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,45,255:15:0	0,21,183:7:0	0,15,167:5:0
+X	1958	.	C	<*>	0	.	DP=29;I16=15,13,0,0,1003,37293,0,0,1649,98041,0,0,493,10825,0,0;QS=3,0;MQSB=0.942064;MQ0F=0	PL:DP:DV	0,45,255:15:0	0,21,191:7:0	0,18,190:6:0
+X	1959	.	T	<*>	0	.	DP=29;I16=16,13,0,0,1112,43258,0,0,1709,101641,0,0,491,10593,0,0;QS=3,0;MQSB=0.940317;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,21,213:7:0	0,18,193:6:0
+X	1960	.	T	<*>	0	.	DP=30;I16=17,13,0,0,1053,37939,0,0,1769,105241,0,0,485,10339,0,0;QS=3,0;MQSB=0.938685;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,21,196:7:0	0,18,186:6:0
+X	1961	.	C	<*>	0	.	DP=30;I16=17,13,0,0,1101,41737,0,0,1769,105241,0,0,480,10122,0,0;QS=3,0;MQSB=0.938685;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,21,195:7:0	0,18,183:6:0
+X	1962	.	T	<*>	0	.	DP=29;I16=17,12,0,0,1134,44582,0,0,1709,101641,0,0,477,9941,0,0;QS=3,0;MQSB=0.931617;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,21,208:7:0	0,18,198:6:0
+X	1963	.	G	<*>	0	.	DP=28;I16=16,12,0,0,1066,41050,0,0,1649,98041,0,0,476,9794,0,0;QS=3,0;MQSB=0.933359;MQ0F=0	PL:DP:DV	0,45,255:15:0	0,21,192:7:0	0,18,188:6:0
+X	1964	.	G	<*>	0	.	DP=28;I16=16,12,0,0,970,34764,0,0,1649,98041,0,0,475,9681,0,0;QS=3,0;MQSB=0.933359;MQ0F=0	PL:DP:DV	0,45,255:15:0	0,21,178:7:0	0,18,169:6:0
+X	1965	.	T	<*>	0	.	DP=29;I16=16,12,0,0,964,34772,0,0,1649,98041,0,0,449,8977,0,0;QS=3,0;MQSB=0.933359;MQ0F=0	PL:DP:DV	0,45,255:15:0	0,21,196:7:0	0,18,171:6:0
+X	1966	.	T	<*>	0	.	DP=29;I16=16,13,0,0,1029,37027,0,0,1709,101641,0,0,474,9558,0,0;QS=3,0;MQSB=0.940317;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,21,191:7:0	0,18,181:6:0
+X	1967	.	A	<*>	0	.	DP=29;I16=16,13,0,0,1030,37234,0,0,1709,101641,0,0,474,9550,0,0;QS=3,0;MQSB=0.940317;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,21,187:7:0	0,18,182:6:0
+X	1968	.	T	<*>	0	.	DP=29;I16=16,13,0,0,1075,40173,0,0,1709,101641,0,0,474,9578,0,0;QS=3,0;MQSB=0.940317;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,21,195:7:0	0,18,190:6:0
+X	1969	.	A	<*>	0	.	DP=28;I16=16,12,0,0,992,35828,0,0,1649,98041,0,0,474,9592,0,0;QS=3,0;MQSB=0.933359;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,18,175:6:0	0,18,186:6:0
+X	1970	.	C	<*>	0	.	DP=28;I16=16,12,0,0,1015,37503,0,0,1649,98041,0,0,474,9642,0,0;QS=3,0;MQSB=0.933359;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,18,170:6:0	0,18,180:6:0
+X	1971	.	A	<*>	0	.	DP=29;I16=16,13,0,0,1073,40273,0,0,1709,101641,0,0,474,9728,0,0;QS=3,0;MQSB=0.940317;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,18,178:6:0	0,21,206:7:0
+X	1972	.	T	<*>	0	.	DP=30;I16=16,14,0,0,1068,38978,0,0,1769,105241,0,0,475,9851,0,0;QS=3,0;MQSB=0.946202;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,18,176:6:0	0,21,203:7:0
+X	1973	.	A	<*>	0	.	DP=30;I16=16,13,0,0,1046,38070,0,0,1740,104400,0,0,452,9388,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,18,172:6:0	0,18,196:6:0
+X	1974	.	A	<*>	0	.	DP=29;I16=16,13,0,0,1086,41474,0,0,1709,101641,0,0,477,10065,0,0;QS=3,0;MQSB=0.940317;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,15,157:5:0	0,21,214:7:0
+X	1975	.	G	<*>	0	.	DP=28;I16=16,12,0,0,1067,41171,0,0,1649,98041,0,0,478,10156,0,0;QS=3,0;MQSB=0.933359;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,12,133:4:0	0,21,195:7:0
+X	1976	.	A	<*>	0	.	DP=28;I16=16,12,0,0,981,34839,0,0,1649,98041,0,0,478,10234,0,0;QS=3,0;MQSB=0.933359;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,12,125:4:0	0,21,199:7:0
+X	1977	.	C	<*>	0	.	DP=28;I16=16,12,0,0,1009,37471,0,0,1649,98041,0,0,477,10297,0,0;QS=3,0;MQSB=0.933359;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,12,132:4:0	0,21,194:7:0
+X	1978	.	A	<*>	0	.	DP=28;I16=16,12,0,0,1082,42132,0,0,1649,98041,0,0,476,10394,0,0;QS=3,0;MQSB=0.933359;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,12,144:4:0	0,21,220:7:0
+X	1979	.	G	<*>	0	.	DP=28;I16=16,11,0,0,1019,38927,0,0,1589,94441,0,0,454,10064,0,0;QS=3,0;MQSB=0.925036;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,12,122:4:0	0,21,208:7:0
+X	1980	.	C	<*>	0	.	DP=27;I16=16,10,0,0,932,34456,0,0,1529,90841,0,0,452,10114,0,0;QS=3,0;MQSB=0.914947;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,9,107:3:0	0,21,197:7:0
+X	1981	.	C	<*>	0	.	DP=28;I16=16,12,0,0,998,36510,0,0,1649,98041,0,0,469,10479,0,0;QS=3,0;MQSB=0.933359;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,9,101:3:0	0,24,219:8:0
+X	1982	.	A	<*>	0	.	DP=29;I16=16,12,0,0,1035,38815,0,0,1649,98041,0,0,472,10548,0,0;QS=3,0;MQSB=0.933359;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,9,110:3:0	0,27,254:9:0
+X	1983	.	G	<*>	0	.	DP=28;I16=16,12,0,0,1048,40322,0,0,1649,98041,0,0,477,10599,0,0;QS=3,0;MQSB=0.933359;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,9,96:3:0	0,27,249:9:0
+X	1984	.	A	<*>	0	.	DP=27;I16=16,11,0,0,1024,39232,0,0,1589,94441,0,0,482,10632,0,0;QS=3,0;MQSB=0.925036;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,6,70:2:0	0,27,255:9:0
+X	1985	.	G	<*>	0	.	DP=27;I16=16,11,0,0,1009,38449,0,0,1589,94441,0,0,487,10695,0,0;QS=3,0;MQSB=0.925036;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,6,66:2:0	0,27,231:9:0
+X	1986	.	A	<*>	0	.	DP=27;I16=16,10,0,0,926,33696,0,0,1560,93600,0,0,466,10112,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,6,76:2:0	0,24,223:8:0
+X	1987	.	A	<*>	0	.	DP=28;I16=17,11,0,0,1034,39088,0,0,1649,98041,0,0,495,10807,0,0;QS=3,0;MQSB=0.923174;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,6,78:2:0	0,27,247:9:0
+X	1988	.	G	<*>	0	.	DP=28;I16=17,11,0,0,1050,39980,0,0,1649,98041,0,0,499,10855,0,0;QS=3,0;MQSB=0.923174;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,6,63:2:0	0,27,239:9:0
+X	1989	.	G	<*>	0	.	DP=28;I16=17,10,0,0,994,37610,0,0,1589,94441,0,0,493,10801,0,0;QS=3,0;MQSB=0.912952;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,6,73:2:0	0,27,237:9:0
+X	1990	.	G	T,<*>	0	.	DP=28;I16=17,9,0,1,965,36359,33,1089,1560,93600,29,841,472,10250,25,625;QS=2.90675,0.0932476,0;SGB=-0.556633;RPB=1;MQB=1;MQSB=0.912952;BQB=1;MQ0F=0	PL:DP:DV	0,48,255,48,255,255:16:0	0,6,71,6,71,71:2:0	2,0,195,26,198,215:9:1
+X	1991	.	A	<*>	0	.	DP=28;I16=17,11,0,0,1017,38203,0,0,1649,98041,0,0,507,10975,0,0;QS=3,0;MQSB=0.923174;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,6,60:2:0	0,27,250:9:0
+X	1992	.	G	<*>	0	.	DP=28;I16=17,11,0,0,1028,38852,0,0,1649,98041,0,0,509,11039,0,0;QS=3,0;MQSB=0.923174;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,6,62:2:0	0,27,231:9:0
+X	1993	.	T	<*>	0	.	DP=28;I16=17,11,0,0,1015,37325,0,0,1649,98041,0,0,511,11131,0,0;QS=3,0;MQSB=0.923174;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,6,59:2:0	0,27,243:9:0
+X	1994	.	T	<*>	0	.	DP=27;I16=16,11,0,0,942,33698,0,0,1589,94441,0,0,514,11250,0,0;QS=3,0;MQSB=0.925036;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,6,54:2:0	0,24,216:8:0
+X	1995	.	G	<*>	0	.	DP=28;I16=16,11,0,0,960,35432,0,0,1620,97200,0,0,492,10770,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,54,255:18:0	0,6,66:2:0	0,21,188:7:0
+X	1996	.	C	<*>	0	.	DP=29;I16=17,12,0,0,1022,37426,0,0,1709,101641,0,0,519,11469,0,0;QS=3,0;MQSB=0.931617;MQ0F=0	PL:DP:DV	0,57,255:19:0	0,6,64:2:0	0,24,192:8:0
+X	1997	.	C	<*>	0	.	DP=29;I16=17,11,0,0,934,32858,0,0,1649,98041,0,0,520,11524,0,0;QS=3,0;MQSB=0.923174;MQ0F=0	PL:DP:DV	0,54,255:18:0	0,6,70:2:0	0,24,193:8:0
+X	1998	.	C	<*>	0	.	DP=29;I16=17,12,0,0,1027,37843,0,0,1709,101641,0,0,522,11562,0,0;QS=3,0;MQSB=0.931617;MQ0F=0	PL:DP:DV	0,57,255:19:0	0,6,69:2:0	0,24,222:8:0
+X	1999	.	A	<*>	0	.	DP=28;I16=17,11,0,0,1073,41493,0,0,1649,98041,0,0,525,11627,0,0;QS=3,0;MQSB=0.923174;MQ0F=0	PL:DP:DV	0,57,255:19:0	0,6,72:2:0	0,21,206:7:0
+X	2000	.	G	<*>	0	.	DP=28;I16=16,11,0,0,1036,40576,0,0,1589,94441,0,0,511,11395,0,0;QS=3,0;MQSB=0.925036;MQ0F=0	PL:DP:DV	0,57,255:19:0	0,6,72:2:0	0,18,168:6:0
+X	2001	.	G	<*>	0	.	DP=28;I16=15,11,0,0,955,35661,0,0,1529,90841,0,0,489,10853,0,0;QS=3,0;MQSB=0.927041;MQ0F=0	PL:DP:DV	0,54,255:18:0	0,6,62:2:0	0,18,172:6:0
+X	2002	.	G	<*>	0	.	DP=28;I16=17,10,0,0,907,32227,0,0,1620,97200,0,0,519,11663,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,57,255:19:0	0,6,53:2:0	0,18,163:6:0
+X	2003	.	T	<*>	0	.	DP=28;I16=17,11,0,0,920,31866,0,0,1649,98041,0,0,541,12163,0,0;QS=3,0;MQSB=0.923174;MQ0F=0	PL:DP:DV	0,57,255:19:0	0,6,49:2:0	0,21,190:7:0
+X	2004	.	G	<*>	0	.	DP=27;I16=16,10,0,0,970,36928,0,0,1560,93600,0,0,530,12110,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,54,255:18:0	0,6,57:2:0	0,18,178:6:0
+X	2005	.	G	<*>	0	.	DP=27;I16=16,10,0,0,868,30936,0,0,1560,93600,0,0,536,12370,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,54,255:18:0	0,6,59:2:0	0,18,153:6:0
+X	2006	.	C	<*>	0	.	DP=27;I16=16,10,0,0,968,37046,0,0,1560,93600,0,0,541,12605,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,54,255:18:0	0,6,73:2:0	0,18,166:6:0
+X	2007	.	A	<*>	0	.	DP=27;I16=16,11,0,0,1000,37396,0,0,1589,94441,0,0,556,12882,0,0;QS=3,0;MQSB=0.925036;MQ0F=0	PL:DP:DV	0,54,255:18:0	0,6,76:2:0	0,21,193:7:0
+X	2008	.	C	<*>	0	.	DP=26;I16=16,10,0,0,964,36892,0,0,1529,90841,0,0,555,12833,0,0;QS=3,0;MQSB=0.914947;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,6,73:2:0	0,21,183:7:0
+X	2009	.	A	<*>	0	.	DP=26;I16=16,10,0,0,997,38955,0,0,1529,90841,0,0,554,12802,0,0;QS=3,0;MQSB=0.914947;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,6,74:2:0	0,21,210:7:0
+X	2010	.	G	<*>	0	.	DP=26;I16=16,9,0,0,936,36208,0,0,1500,90000,0,0,542,12640,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,6,73:2:0	0,18,169:6:0
+X	2011	.	C	<*>	0	.	DP=26;I16=16,9,0,0,966,37960,0,0,1500,90000,0,0,541,12617,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,6,74:2:0	0,18,175:6:0
+X	2012	.	A	<*>	0	.	DP=27;I16=16,11,0,0,956,35018,0,0,1589,94441,0,0,548,12676,0,0;QS=3,0;MQSB=0.925036;MQ0F=0	PL:DP:DV	0,54,255:18:0	0,6,74:2:0	0,21,189:7:0
+X	2013	.	C	<*>	0	.	DP=27;I16=15,10,0,0,876,31370,0,0,1500,90000,0,0,514,11950,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,6,69:2:0	0,18,160:6:0
+X	2014	.	G	<*>	0	.	DP=27;I16=17,10,0,0,903,31239,0,0,1589,94441,0,0,545,12591,0,0;QS=3,0;MQSB=0.912952;MQ0F=0	PL:DP:DV	0,54,255:18:0	0,9,80:3:0	0,18,160:6:0
+X	2015	.	T	<*>	0	.	DP=27;I16=17,10,0,0,999,37507,0,0,1589,94441,0,0,545,12577,0,0;QS=3,0;MQSB=0.912952;MQ0F=0	PL:DP:DV	0,54,255:18:0	0,9,95:3:0	0,18,178:6:0
+X	2016	.	T	<*>	0	.	DP=27;I16=17,10,0,0,971,35649,0,0,1589,94441,0,0,545,12583,0,0;QS=3,0;MQSB=0.912952;MQ0F=0	PL:DP:DV	0,54,255:18:0	0,9,93:3:0	0,18,178:6:0
+X	2017	.	G	<*>	0	.	DP=28;I16=17,11,0,0,1013,37849,0,0,1649,98041,0,0,545,12609,0,0;QS=3,0;MQSB=0.923174;MQ0F=0	PL:DP:DV	0,57,255:19:0	0,9,91:3:0	0,18,172:6:0
+X	2018	.	C	<*>	0	.	DP=28;I16=17,11,0,0,1060,41414,0,0,1649,98041,0,0,546,12656,0,0;QS=3,0;MQSB=0.923174;MQ0F=0	PL:DP:DV	0,57,255:19:0	0,9,97:3:0	0,18,169:6:0
+X	2019	.	T	<*>	0	.	DP=28;I16=17,11,0,0,1083,42253,0,0,1649,98041,0,0,547,12725,0,0;QS=3,0;MQSB=0.923174;MQ0F=0	PL:DP:DV	0,57,255:19:0	0,9,106:3:0	0,18,187:6:0
+X	2020	.	G	<*>	0	.	DP=29;I16=18,11,0,0,1095,42063,0,0,1678,98882,0,0,548,12816,0,0;QS=3,0;MQSB=0.987702;MQ0F=0	PL:DP:DV	0,60,255:20:0	0,9,85:3:0	0,18,175:6:0
+X	2021	.	C	<*>	0	.	DP=29;I16=18,11,0,0,1081,41535,0,0,1709,101641,0,0,551,12877,0,0;QS=3,0;MQSB=0.969907;MQ0F=0	PL:DP:DV	0,63,255:21:0	0,9,97:3:0	0,15,167:5:0
+X	2022	.	C	<*>	0	.	DP=30;I16=19,11,0,0,1115,42003,0,0,1769,105241,0,0,555,12907,0,0;QS=3,0;MQSB=0.972375;MQ0F=0	PL:DP:DV	0,63,255:21:0	0,9,92:3:0	0,18,177:6:0
+X	2023	.	A	<*>	0	.	DP=30;I16=19,10,0,0,1063,39991,0,0,1709,101641,0,0,549,12837,0,0;QS=3,0;MQSB=0.974027;MQ0F=0	PL:DP:DV	0,60,255:20:0	0,9,96:3:0	0,18,186:6:0
+X	2024	.	G	<*>	0	.	DP=32;I16=20,12,0,0,1168,43872,0,0,1889,112441,0,0,564,12982,0,0;QS=3,0;MQSB=0.973096;MQ0F=0	PL:DP:DV	0,63,255:21:0	0,9,92:3:0	0,24,203:8:0
+X	2025	.	T	<*>	0	.	DP=32;I16=20,12,0,0,1150,42122,0,0,1889,112441,0,0,569,12981,0,0;QS=3,0;MQSB=0.973096;MQ0F=0	PL:DP:DV	0,63,255:21:0	0,9,87:3:0	0,24,226:8:0
+X	2026	.	T	<*>	0	.	DP=32;I16=20,12,0,0,1130,40724,0,0,1889,112441,0,0,572,12908,0,0;QS=3,0;MQSB=0.973096;MQ0F=0	PL:DP:DV	0,63,255:21:0	0,9,94:3:0	0,24,208:8:0
+X	2027	.	A	<*>	0	.	DP=32;I16=19,12,0,0,1121,40871,0,0,1829,108841,0,0,550,12240,0,0;QS=3,0;MQSB=0.970829;MQ0F=0	PL:DP:DV	0,63,255:21:0	0,9,84:3:0	0,21,207:7:0
+X	2028	.	C	<*>	0	.	DP=32;I16=20,12,0,0,1242,48548,0,0,1889,112441,0,0,577,12803,0,0;QS=3,0;MQSB=0.973096;MQ0F=0	PL:DP:DV	0,63,255:21:0	0,9,94:3:0	0,24,228:8:0
+X	2029	.	T	<*>	0	.	DP=32;I16=20,12,0,0,1229,47605,0,0,1889,112441,0,0,578,12724,0,0;QS=3,0;MQSB=0.973096;MQ0F=0	PL:DP:DV	0,63,255:21:0	0,9,102:3:0	0,24,236:8:0
+X	2030	.	G	<*>	0	.	DP=32;I16=20,12,0,0,1222,47140,0,0,1889,112441,0,0,579,12679,0,0;QS=3,0;MQSB=0.973096;MQ0F=0	PL:DP:DV	0,63,255:21:0	0,9,93:3:0	0,24,216:8:0
+X	2031	.	C	<*>	0	.	DP=31;I16=19,12,0,0,1150,43656,0,0,1829,108841,0,0,581,12667,0,0;QS=3,0;MQSB=0.970829;MQ0F=0	PL:DP:DV	0,60,255:20:0	0,9,96:3:0	0,24,204:8:0
+X	2032	.	C	<*>	0	.	DP=31;I16=19,12,0,0,1157,44035,0,0,1829,108841,0,0,583,12687,0,0;QS=3,0;MQSB=0.970829;MQ0F=0	PL:DP:DV	0,60,255:20:0	0,9,90:3:0	0,24,210:8:0
+X	2033	.	A	<*>	0	.	DP=30;I16=19,11,0,0,1091,40223,0,0,1769,105241,0,0,585,12689,0,0;QS=3,0;MQSB=0.972375;MQ0F=0	PL:DP:DV	0,60,255:20:0	0,9,93:3:0	0,21,203:7:0
+X	2034	.	T	<*>	0	.	DP=30;I16=19,11,0,0,1104,41498,0,0,1769,105241,0,0,587,12723,0,0;QS=3,0;MQSB=0.972375;MQ0F=0	PL:DP:DV	0,60,255:20:0	0,9,91:3:0	0,21,208:7:0
+X	2035	.	T	<*>	0	.	DP=29;I16=18,11,0,0,1084,41024,0,0,1709,101641,0,0,589,12739,0,0;QS=3,0;MQSB=0.969907;MQ0F=0	PL:DP:DV	0,60,255:20:0	0,6,69:2:0	0,21,211:7:0
+X	2036	.	T	<*>	0	.	DP=29;I16=18,11,0,0,1080,40612,0,0,1709,101641,0,0,591,12787,0,0;QS=3,0;MQSB=0.969907;MQ0F=0	PL:DP:DV	0,60,255:20:0	0,6,67:2:0	0,21,216:7:0
+X	2037	.	T	<*>	0	.	DP=29;I16=18,11,0,0,1082,40956,0,0,1709,101641,0,0,592,12818,0,0;QS=3,0;MQSB=0.969907;MQ0F=0	PL:DP:DV	0,60,255:20:0	0,6,69:2:0	0,21,217:7:0
+X	2038	.	C	<*>	0	.	DP=29;I16=18,11,0,0,1117,43573,0,0,1709,101641,0,0,592,12832,0,0;QS=3,0;MQSB=0.969907;MQ0F=0	PL:DP:DV	0,60,255:20:0	0,6,69:2:0	0,21,211:7:0
+X	2039	.	A	<*>	0	.	DP=29;I16=18,11,0,0,1067,39581,0,0,1709,101641,0,0,592,12878,0,0;QS=3,0;MQSB=0.969907;MQ0F=0	PL:DP:DV	0,60,255:20:0	0,6,72:2:0	0,21,212:7:0
+X	2040	.	C	<*>	0	.	DP=29;I16=18,11,0,0,1077,40469,0,0,1709,101641,0,0,590,12856,0,0;QS=3,0;MQSB=0.969907;MQ0F=0	PL:DP:DV	0,60,255:20:0	0,6,69:2:0	0,21,196:7:0
+X	2041	.	G	A,<*>	0	.	DP=31;I16=6,5,12,7,389,14023,721,28149,660,39600,1109,65641,235,5607,353,7259;QS=0.917304,2.0827,0;VDB=0.816435;SGB=-4.18892;RPB=0.88473;MQB=0.972375;MQSB=0.968257;BQB=0.311275;MQ0F=0	PL:DP:DV	229,0,212,255,245,255:21:11	32,0,24,35,27,59:2:1	223,21,0,223,21,223:7:7
+X	2042	.	G	<*>	0	.	DP=32;I16=18,14,0,0,1189,45617,0,0,1889,112441,0,0,588,12910,0,0;QS=3,0;MQSB=0.965264;MQ0F=0	PL:DP:DV	0,66,255:22:0	0,9,86:3:0	0,21,206:7:0
+X	2043	.	G	<*>	0	.	DP=32;I16=17,14,0,0,1115,41585,0,0,1829,108841,0,0,581,12891,0,0;QS=3,0;MQSB=0.962133;MQ0F=0	PL:DP:DV	0,63,255:21:0	0,9,90:3:0	0,21,197:7:0
+X	2044	.	C	<*>	0	.	DP=32;I16=18,14,0,0,1213,47029,0,0,1889,112441,0,0,588,13006,0,0;QS=3,0;MQSB=0.965264;MQ0F=0	PL:DP:DV	0,66,255:22:0	0,9,85:3:0	0,21,207:7:0
+X	2045	.	A	<*>	0	.	DP=32;I16=18,14,0,0,1181,44527,0,0,1889,112441,0,0,588,13108,0,0;QS=3,0;MQSB=0.965264;MQ0F=0	PL:DP:DV	0,66,255:22:0	0,9,83:3:0	0,21,213:7:0
+X	2046	.	T	<*>	0	.	DP=32;I16=18,14,0,0,1197,45135,0,0,1889,112441,0,0,587,13195,0,0;QS=3,0;MQSB=0.965264;MQ0F=0	PL:DP:DV	0,66,255:22:0	0,9,103:3:0	0,21,216:7:0
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+X	2729	.	T	<*>	0	.	DP=25;I16=12,13,0,0,871,31019,0,0,1407,81723,0,0,469,10233,0,0;QS=3,0;MQSB=0.619223;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,21,189:7:0	0,6,62:2:0
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+X	2735	.	T	<*>	0	.	DP=26;I16=13,12,0,0,955,36875,0,0,1438,84482,0,0,451,9877,0,0;QS=3,0;MQSB=0.778801;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,24,228:8:0	0,3,41:1:0
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+X	2737	.	T	<*>	0	.	DP=26;I16=13,13,0,0,967,36581,0,0,1467,85323,0,0,475,10403,0,0;QS=3,0;MQSB=0.606531;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,24,228:8:0	0,6,64:2:0
+X	2738	.	T	<*>	0	.	DP=26;I16=13,13,0,0,895,31873,0,0,1467,85323,0,0,474,10374,0,0;QS=3,0;MQSB=0.606531;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,24,201:8:0	0,6,47:2:0
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+X	2760	.	T	<*>	0	.	DP=25;I16=14,11,0,0,907,33965,0,0,1438,84482,0,0,457,10275,0,0;QS=3,0;MQSB=0.745495;MQ0F=0	PL:DP:DV	0,39,255:13:0	0,21,204:7:0	0,15,150:5:0
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+X	2765	.	T	<*>	0	.	DP=24;I16=12,11,0,0,853,32173,0,0,1318,77282,0,0,457,10469,0,0;QS=3,0;MQSB=0.7613;MQ0F=0	PL:DP:DV	0,36,255:12:0	0,15,154:5:0	0,18,189:6:0
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+X	2767	.	T	<*>	0	.	DP=24;I16=12,12,0,0,905,34757,0,0,1378,80882,0,0,458,10510,0,0;QS=3,0;MQSB=0.786628;MQ0F=0	PL:DP:DV	0,36,255:12:0	0,15,153:5:0	0,21,217:7:0
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+X	2770	.	T	<*>	0	.	DP=23;I16=11,12,0,0,828,30854,0,0,1318,77282,0,0,459,10471,0,0;QS=3,0;MQSB=0.795196;MQ0F=0	PL:DP:DV	0,33,255:11:0	0,15,152:5:0	0,21,199:7:0
+X	2771	.	T	<*>	0	.	DP=23;I16=11,11,0,0,817,30957,0,0,1258,73682,0,0,454,10456,0,0;QS=3,0;MQSB=0.770381;MQ0F=0	PL:DP:DV	0,33,255:11:0	0,15,154:5:0	0,18,198:6:0
+X	2772	.	T	<*>	0	.	DP=23;I16=11,12,0,0,856,32206,0,0,1318,77282,0,0,459,10511,0,0;QS=3,0;MQSB=0.795196;MQ0F=0	PL:DP:DV	0,33,255:11:0	0,15,160:5:0	0,21,210:7:0
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+X	3194	.	T	C,<*>	0	.	DP=21;I16=10,10,1,0,730,26992,18,324,1169,69241,29,841,332,7168,25,625;QS=2.95652,0.0434783,0;SGB=-0.556633;RPB=1;MQB=1;MQSB=0.99938;BQB=1;MQ0F=0	PL:DP:DV	0,18,255,33,255,255:12:1	0,9,98,9,98,98:3:0	0,18,178,18,178,178:6:0
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+X	3212	.	T	<*>	0	.	DP=17;I16=10,6,0,0,575,21295,0,0,960,57600,0,0,316,6964,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,27,222:9:0	0,9,100:3:0	0,12,144:4:0
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+X	3230	.	T	<*>	0	.	DP=19;I16=12,6,0,0,669,25441,0,0,1049,62041,0,0,261,5187,0,0;QS=3,0;MQSB=0.961295;MQ0F=0	PL:DP:DV	0,33,255:11:0	0,9,107:3:0	0,12,139:4:0
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+X	3237	.	T	<*>	0	.	DP=17;I16=11,6,0,0,589,21235,0,0,989,58441,0,0,273,5573,0,0;QS=3,0;MQSB=0.955563;MQ0F=0	PL:DP:DV	0,27,230:9:0	0,12,102:4:0	0,12,136:4:0
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+X	3239	.	T	<*>	0	.	DP=17;I16=11,6,0,0,574,20204,0,0,989,58441,0,0,273,5645,0,0;QS=3,0;MQSB=0.955563;MQ0F=0	PL:DP:DV	0,27,220:9:0	0,12,107:4:0	0,12,131:4:0
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+X	3242	.	T	<*>	0	.	DP=19;I16=12,7,0,0,655,23279,0,0,1140,68400,0,0,277,5911,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,30,252:10:0	0,12,104:4:0	0,15,152:5:0
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+X	3528	.	T	<*>	0	.	DP=31;I16=13,16,0,0,1076,41782,0,0,1678,98882,0,0,561,12369,0,0;QS=3,0;MQSB=0.997839;MQ0F=0	PL:DP:DV	0,54,255:18:0	0,18,193:6:0	0,15,152:5:0
+X	3529	.	T	<*>	0	.	DP=31;I16=12,16,0,0,1016,38674,0,0,1649,98041,0,0,550,12290,0,0;QS=3,0;MQSB=0.96195;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,18,184:6:0	0,15,154:5:0
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+X	3533	.	T	<*>	0	.	DP=31;I16=13,17,0,0,1074,39206,0,0,1738,102482,0,0,595,13457,0,0;QS=3,0;MQSB=0.996503;MQ0F=0	PL:DP:DV	0,54,255:18:0	0,18,180:6:0	0,18,176:6:0
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+X	3535	.	T	<*>	0	.	DP=31;I16=14,17,0,0,1042,36456,0,0,1767,103323,0,0,624,14314,0,0;QS=3,0;MQSB=0.924242;MQ0F=0	PL:DP:DV	0,57,255:19:0	0,18,162:6:0	0,18,164:6:0
+X	3536	.	C	<*>	0	.	DP=31;I16=13,17,0,0,1102,41182,0,0,1738,102482,0,0,602,13842,0,0;QS=3,0;MQSB=0.996503;MQ0F=0	PL:DP:DV	0,54,255:18:0	0,18,178:6:0	0,18,180:6:0
+X	3537	.	C	<*>	0	.	DP=32;I16=13,17,0,0,1142,43828,0,0,1769,105241,0,0,598,13854,0,0;QS=3,0;MQSB=0.963674;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,21,194:7:0	0,18,185:6:0
+X	3538	.	T	<*>	0	.	DP=32;I16=14,17,0,0,1151,43471,0,0,1798,106082,0,0,603,13923,0,0;QS=3,0;MQSB=0.998229;MQ0F=0	PL:DP:DV	0,54,255:18:0	0,21,211:7:0	0,18,185:6:0
+X	3539	.	C	<*>	0	.	DP=32;I16=12,17,0,0,1077,40959,0,0,1709,101641,0,0,600,13994,0,0;QS=3,0;MQSB=0.965321;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,18,170:6:0	0,18,173:6:0
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+X	3551	.	T	<*>	0	.	DP=30;I16=13,16,0,0,1026,36844,0,0,1709,101641,0,0,613,14295,0,0;QS=3,0;MQSB=0.960189;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,21,192:7:0	0,15,162:5:0
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+X	3553	.	T	A,<*>	0	.	DP=30;I16=13,16,1,0,1047,38333,20,400,1709,101641,29,841,616,14398,16,256;QS=2.96795,0.0320513,0;SGB=-0.556633;RPB=1;MQB=1;MQSB=0.999136;BQB=1;MQ0F=0	PL:DP:DV	0,34,255,51,255,255:18:1	0,18,178,18,178,178:6:0	0,18,183,18,183,183:6:0
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+X	3559	.	T	<*>	0	.	DP=30;I16=14,16,0,0,1086,40202,0,0,1769,105241,0,0,619,14341,0,0;QS=3,0;MQSB=0.958545;MQ0F=0	PL:DP:DV	0,54,255:18:0	0,18,171:6:0	0,18,192:6:0
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+X	3564	.	T	<*>	0	.	DP=31;I16=15,15,0,0,1132,43298,0,0,1769,105241,0,0,610,13932,0,0;QS=3,0;MQSB=0.952765;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,18,192:6:0	0,21,214:7:0
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+X	3570	.	T	<*>	0	.	DP=30;I16=14,15,0,0,1029,37527,0,0,1709,101641,0,0,572,12730,0,0;QS=3,0;MQSB=0.954405;MQ0F=0	PL:DP:DV	0,54,255:18:0	0,12,136:4:0	0,21,213:7:0
+X	3571	.	C	<*>	0	.	DP=28;I16=13,15,0,0,1066,41192,0,0,1649,98041,0,0,568,12564,0,0;QS=3,0;MQSB=0.956162;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,12,138:4:0	0,21,215:7:0
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+X	3574	.	T	<*>	0	.	DP=29;I16=13,16,0,0,1104,42220,0,0,1709,101641,0,0,552,11942,0,0;QS=3,0;MQSB=0.960189;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,15,175:5:0	0,21,218:7:0
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+X	3774	.	T	<*>	0	.	DP=25;I16=15,10,0,0,895,33455,0,0,1278,70004,0,0,485,10903,0,0;QS=3,0;MQSB=0.624282;MQ0F=0	PL:DP:DV	0,42,253:14:0	0,18,129:6:0	0,15,178:5:0
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+X	3786	.	T	<*>	0	.	DP=28;I16=16,11,0,0,935,35697,0,0,1375,74973,0,0,490,10774,0,0;QS=3,0;MQSB=0.467219;MQ0F=0	PL:DP:DV	0,48,250:16:0	0,18,145:6:0	0,15,186:5:0
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+X	3790	.	T	<*>	0	.	DP=26;I16=13,10,0,0,829,32293,0,0,1231,68535,0,0,435,9359,0,0;QS=3,0;MQSB=0.445672;MQ0F=0	PL:DP:DV	0,39,255:13:0	0,18,150:6:0	0,12,159:4:0
+X	3791	.	T	<*>	0	.	DP=26;I16=15,10,0,0,887,34725,0,0,1301,72235,0,0,478,10336,0,0;QS=3,0;MQSB=0.382304;MQ0F=0	PL:DP:DV	0,45,255:15:0	0,18,136:6:0	0,12,159:4:0
+X	3792	.	G	A,<*>	0	.	DP=26;I16=14,8,1,0,809,32805,38,1444,1175,66425,37,1369,417,8991,22,484;QS=2.92629,0.0737052,0;SGB=-0.556633;RPB=1;MQB=1;MQSB=0.195278;BQB=1;MQ0F=0	PL:DP:DV	0,8,238,42,241,255:15:1	0,12,109,12,109,109:4:0	0,12,157,12,157,157:4:0
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+X	3794	.	C	<*>	0	.	DP=26;I16=15,9,0,0,845,33023,0,0,1241,68635,0,0,438,9324,0,0;QS=3,0;MQSB=0.439649;MQ0F=0	PL:DP:DV	0,45,255:15:0	0,15,120:5:0	0,12,157:4:0
+X	3795	.	C	<*>	0	.	DP=26;I16=14,9,0,0,865,35649,0,0,1231,68535,0,0,408,8622,0,0;QS=3,0;MQSB=0.563599;MQ0F=0	PL:DP:DV	0,42,255:14:0	0,15,132:5:0	0,12,161:4:0
+X	3796	.	T	<*>	0	.	DP=27;I16=15,11,0,0,964,38998,0,0,1361,75835,0,0,453,9821,0,0;QS=3,0;MQSB=0.334895;MQ0F=0	PL:DP:DV	0,45,255:15:0	0,21,149:7:0	0,12,164:4:0
+X	3797	.	A	<*>	0	.	DP=27;I16=15,10,0,0,848,32392,0,0,1301,72235,0,0,424,9172,0,0;QS=3,0;MQSB=0.382304;MQ0F=0	PL:DP:DV	0,45,255:15:0	0,18,124:6:0	0,12,159:4:0
+X	3798	.	T	<*>	0	.	DP=27;I16=14,11,0,0,921,37161,0,0,1301,72235,0,0,430,9554,0,0;QS=3,0;MQSB=0.283586;MQ0F=0	PL:DP:DV	0,42,255:14:0	0,21,148:7:0	0,12,165:4:0
+X	3799	.	T	<*>	0	.	DP=27;I16=15,11,0,0,913,35929,0,0,1361,75835,0,0,439,9729,0,0;QS=3,0;MQSB=0.334895;MQ0F=0	PL:DP:DV	0,45,255:15:0	0,21,150:7:0	0,12,161:4:0
+X	3800	.	C	<*>	0	.	DP=26;I16=13,10,0,0,866,36182,0,0,1181,65035,0,0,406,9092,0,0;QS=3,0;MQSB=0.272532;MQ0F=0	PL:DP:DV	0,42,255:14:0	0,15,104:5:0	0,12,161:4:0
+X	3801	.	T	<*>	0	.	DP=23;I16=12,10,0,0,804,33600,0,0,1121,61435,0,0,430,9750,0,0;QS=3,0;MQSB=0.217267;MQ0F=0	PL:DP:DV	0,42,255:14:0	0,15,99:5:0	0,9,133:3:0
+X	3802	.	G	<*>	0	.	DP=22;I16=10,9,0,0,730,30516,0,0,994,54486,0,0,380,8550,0,0;QS=3,0;MQSB=0.472367;MQ0F=0	PL:DP:DV	0,36,255:12:0	0,12,106:4:0	0,9,130:3:0
+X	3803	.	G	<*>	0	.	DP=22;I16=11,9,0,0,703,27393,0,0,1051,57735,0,0,405,9241,0,0;QS=3,0;MQSB=0.372419;MQ0F=0	PL:DP:DV	0,39,249:13:0	0,12,92:4:0	0,9,129:3:0
+X	3804	.	A	<*>	0	.	DP=22;I16=11,9,0,0,740,30360,0,0,1051,57735,0,0,404,9274,0,0;QS=3,0;MQSB=0.372419;MQ0F=0	PL:DP:DV	0,39,255:13:0	0,12,98:4:0	0,9,132:3:0
+X	3805	.	C	<*>	0	.	DP=22;I16=12,9,0,0,737,29243,0,0,1061,57835,0,0,428,9950,0,0;QS=3,0;MQSB=0.262932;MQ0F=0	PL:DP:DV	0,42,255:14:0	0,12,81:4:0	0,9,130:3:0
+X	3806	.	A	<*>	0	.	DP=22;I16=12,9,0,0,798,32550,0,0,1061,57835,0,0,426,9968,0,0;QS=3,0;MQSB=0.262932;MQ0F=0	PL:DP:DV	0,42,255:14:0	0,12,105:4:0	0,9,128:3:0
+X	3807	.	C	<*>	0	.	DP=22;I16=10,9,0,0,664,25304,0,0,994,54486,0,0,377,8885,0,0;QS=3,0;MQSB=0.472367;MQ0F=0	PL:DP:DV	0,36,255:12:0	0,12,83:4:0	0,9,115:3:0
+X	3808	.	G	<*>	0	.	DP=21;I16=9,9,0,0,653,25297,0,0,957,53117,0,0,375,8873,0,0;QS=3,0;MQSB=0.597145;MQ0F=0	PL:DP:DV	0,33,233:11:0	0,12,109:4:0	0,9,132:3:0
+X	3809	.	T	<*>	0	.	DP=22;I16=11,10,0,0,779,32151,0,0,1084,60066,0,0,416,9810,0,0;QS=3,0;MQSB=0.285029;MQ0F=0	PL:DP:DV	0,39,249:13:0	0,12,115:4:0	0,12,161:4:0
+X	3810	.	C	<*>	0	.	DP=23;I16=9,11,0,0,811,34815,0,0,1077,60317,0,0,369,8739,0,0;QS=3,0;MQSB=0.499893;MQ0F=0	PL:DP:DV	0,36,255:12:0	0,12,112:4:0	0,12,153:4:0
+X	3811	.	A	C,<*>	0	.	DP=23;I16=9,11,2,0,777,32631,39,785,1077,60317,67,3349,367,8669,42,914;QS=2.94104,0.0589569,0;VDB=0.18;SGB=0.346553;RPB=0.425;MQB=0.25;MQSB=0.246128;BQB=0.025;MQ0F=0	PL:DP:DV	0,15,248,36,254,255:14:2	0,12,116,12,116,116:4:0	0,12,158,12,158,158:4:0
+X	3812	.	T	<*>	0	.	DP=23;I16=10,11,0,0,802,32860,0,0,1084,60066,0,0,405,9447,0,0;QS=3,0;MQSB=0.187115;MQ0F=0	PL:DP:DV	0,39,255:13:0	0,12,114:4:0	0,12,160:4:0
+X	3813	.	A	<*>	0	.	DP=22;I16=10,11,0,0,815,35077,0,0,1084,60066,0,0,402,9330,0,0;QS=3,0;MQSB=0.187115;MQ0F=0	PL:DP:DV	0,39,255:13:0	0,12,119:4:0	0,12,170:4:0
+X	3814	.	G	<*>	0	.	DP=21;I16=8,11,0,0,775,33731,0,0,1037,58597,0,0,375,8605,0,0;QS=3,0;MQSB=0.41781;MQ0F=0	PL:DP:DV	0,33,255:11:0	0,12,113:4:0	0,12,163:4:0
+X	3815	.	A	<*>	0	.	DP=20;I16=8,11,0,0,708,29130,0,0,1010,57328,0,0,397,9049,0,0;QS=3,0;MQSB=0.373354;MQ0F=0	PL:DP:DV	0,33,239:11:0	0,12,110:4:0	0,12,162:4:0
+X	3816	.	A	<*>	0	.	DP=20;I16=8,11,0,0,729,31027,0,0,1010,57328,0,0,395,8933,0,0;QS=3,0;MQSB=0.373354;MQ0F=0	PL:DP:DV	0,33,248:11:0	0,12,104:4:0	0,12,160:4:0
+X	3817	.	A	<*>	0	.	DP=20;I16=8,11,0,0,752,31580,0,0,1010,57328,0,0,393,8833,0,0;QS=3,0;MQSB=0.373354;MQ0F=0	PL:DP:DV	0,33,255:11:0	0,12,110:4:0	0,12,161:4:0
+X	3818	.	T	<*>	0	.	DP=20;I16=8,11,0,0,728,30466,0,0,1010,57328,0,0,391,8749,0,0;QS=3,0;MQSB=0.373354;MQ0F=0	PL:DP:DV	0,33,252:11:0	0,12,115:4:0	0,12,160:4:0
+X	3819	.	A	<*>	0	.	DP=21;I16=9,11,0,0,790,34094,0,0,1039,58169,0,0,389,8681,0,0;QS=3,0;MQSB=0.247381;MQ0F=0	PL:DP:DV	0,36,255:12:0	0,12,121:4:0	0,12,167:4:0
+X	3820	.	G	<*>	0	.	DP=21;I16=9,11,0,0,788,33636,0,0,1039,58169,0,0,388,8630,0,0;QS=3,0;MQSB=0.247381;MQ0F=0	PL:DP:DV	0,36,255:12:0	0,12,112:4:0	0,12,157:4:0
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+X	3823	.	T	<*>	0	.	DP=22;I16=9,11,0,0,753,30705,0,0,1042,58520,0,0,380,8460,0,0;QS=3,0;MQSB=0.434285;MQ0F=0	PL:DP:DV	0,36,255:12:0	0,12,102:4:0	0,12,163:4:0
+X	3824	.	C	<*>	0	.	DP=22;I16=10,11,0,0,802,32368,0,0,1099,61769,0,0,384,8456,0,0;QS=3,0;MQSB=0.317882;MQ0F=0	PL:DP:DV	0,39,255:13:0	0,12,105:4:0	0,12,159:4:0
+X	3825	.	C	<*>	0	.	DP=23;I16=10,11,0,0,813,33955,0,0,1079,59889,0,0,379,8387,0,0;QS=3,0;MQSB=0.317882;MQ0F=0	PL:DP:DV	0,36,255:12:0	0,15,130:5:0	0,12,157:4:0
+X	3826	.	T	<*>	0	.	DP=23;I16=11,11,0,0,827,34611,0,0,1136,63138,0,0,381,8357,0,0;QS=3,0;MQSB=0.232836;MQ0F=0	PL:DP:DV	0,39,255:13:0	0,15,133:5:0	0,12,155:4:0
+X	3827	.	G	<*>	0	.	DP=23;I16=11,10,0,0,820,34130,0,0,1076,59538,0,0,355,7715,0,0;QS=3,0;MQSB=0.269397;MQ0F=0	PL:DP:DV	0,39,255:13:0	0,12,121:4:0	0,12,162:4:0
+X	3828	.	C	<*>	0	.	DP=23;I16=11,10,0,0,805,33147,0,0,1076,59538,0,0,354,7720,0,0;QS=3,0;MQSB=0.269397;MQ0F=0	PL:DP:DV	0,39,255:13:0	0,12,114:4:0	0,12,157:4:0
+X	3829	.	A	<*>	0	.	DP=22;I16=9,11,0,0,763,31295,0,0,1069,59789,0,0,369,8241,0,0;QS=3,0;MQSB=0.477679;MQ0F=0	PL:DP:DV	0,33,255:11:0	0,15,132:5:0	0,12,158:4:0
+X	3830	.	A	<*>	0	.	DP=23;I16=11,11,0,0,825,32693,0,0,1136,63138,0,0,377,8321,0,0;QS=3,0;MQSB=0.232836;MQ0F=0	PL:DP:DV	0,39,255:13:0	0,15,143:5:0	0,12,150:4:0
+X	3831	.	C	A,<*>	0	.	DP=23;I16=10,11,1,0,802,32198,14,196,1126,63038,10,100,370,8294,7,49;QS=2.97758,0.0224215,0;SGB=-0.556633;RPB=1;MQB=1;MQSB=0.232836;BQB=1;MQ0F=0	PL:DP:DV	0,27,255,36,255,255:13:1	0,15,134,15,134,134:5:0	0,12,149,12,149,149:4:0
+X	3832	.	A	<*>	0	.	DP=24;I16=12,11,0,0,836,32436,0,0,1196,66738,0,0,377,8389,0,0;QS=3,0;MQSB=0.291845;MQ0F=0	PL:DP:DV	0,42,255:14:0	0,15,136:5:0	0,12,139:4:0
+X	3833	.	C	<*>	0	.	DP=23;I16=10,11,0,0,690,24938,0,0,1076,59538,0,0,377,8409,0,0;QS=3,0;MQSB=0.175325;MQ0F=0	PL:DP:DV	0,36,249:12:0	0,15,113:5:0	0,12,131:4:0
+X	3834	.	G	<*>	0	.	DP=22;I16=9,10,0,0,684,26250,0,0,1037,58597,0,0,357,8079,0,0;QS=3,0;MQSB=0.124514;MQ0F=0	PL:DP:DV	0,33,242:11:0	0,12,122:4:0	0,12,156:4:0
+X	3835	.	T	<*>	0	.	DP=22;I16=10,11,0,0,773,30373,0,0,1076,59538,0,0,381,8475,0,0;QS=3,0;MQSB=0.175325;MQ0F=0	PL:DP:DV	0,36,255:12:0	0,15,140:5:0	0,12,153:4:0
+X	3836	.	G	C,<*>	0	.	DP=24;I16=10,12,1,0,833,33183,14,196,1132,61648,10,100,378,8412,2,4;QS=2.97647,0.0235294,0;SGB=-0.556633;RPB=1;MQB=1;MQSB=0.251407;BQB=1;MQ0F=0	PL:DP:DV	0,27,255,36,255,255:13:1	0,15,149,15,149,149:5:0	0,15,188,15,188,188:5:0
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+X	3838	.	C	<*>	0	.	DP=24;I16=10,14,0,0,817,28975,0,0,1202,65348,0,0,409,8945,0,0;QS=3,0;MQSB=0.122456;MQ0F=0	PL:DP:DV	0,39,255:13:0	0,18,143:6:0	0,15,148:5:0
+X	3839	.	C	<*>	0	.	DP=23;I16=9,13,0,0,688,22248,0,0,1132,61648,0,0,386,8238,0,0;QS=3,0;MQSB=0.248197;MQ0F=0	PL:DP:DV	0,36,255:12:0	0,18,123:6:0	0,12,112:4:0
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+X	3841	.	T	<*>	0	.	DP=23;I16=9,14,0,0,867,33103,0,0,1192,65248,0,0,414,8734,0,0;QS=3,0;MQSB=0.211072;MQ0F=0	PL:DP:DV	0,36,255:12:0	0,18,167:6:0	0,15,162:5:0
+X	3842	.	C	<*>	0	.	DP=23;I16=9,14,0,0,890,34728,0,0,1192,65248,0,0,415,8689,0,0;QS=3,0;MQSB=0.211072;MQ0F=0	PL:DP:DV	0,36,255:12:0	0,18,167:6:0	0,15,159:5:0
+X	3843	.	T	<*>	0	.	DP=24;I16=9,14,0,0,896,35122,0,0,1192,65248,0,0,416,8674,0,0;QS=3,0;MQSB=0.211072;MQ0F=0	PL:DP:DV	0,36,255:12:0	0,18,164:6:0	0,15,159:5:0
+X	3844	.	G	<*>	0	.	DP=26;I16=10,16,0,0,959,35715,0,0,1372,76048,0,0,442,9314,0,0;QS=3,0;MQSB=0.220358;MQ0F=0	PL:DP:DV	0,39,255:13:0	0,21,177:7:0	0,18,172:6:0
+X	3845	.	T	<*>	0	.	DP=26;I16=10,16,0,0,970,36442,0,0,1372,76048,0,0,444,9310,0,0;QS=3,0;MQSB=0.220358;MQ0F=0	PL:DP:DV	0,39,255:13:0	0,21,186:7:0	0,18,166:6:0
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+X	3868	.	T	<*>	0	.	DP=33;I16=11,22,0,0,1255,48141,0,0,1792,101248,0,0,590,12494,0,0;QS=3,0;MQSB=0.161533;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,21,202:7:0	0,27,221:9:0
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+X	3870	.	T	<*>	0	.	DP=34;I16=11,23,0,0,1262,47808,0,0,1852,104848,0,0,608,12932,0,0;QS=3,0;MQSB=0.149071;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,24,215:8:0	0,27,211:9:0
+X	3871	.	T	<*>	0	.	DP=36;I16=11,25,0,0,1341,50655,0,0,1972,112048,0,0,617,13157,0,0;QS=3,0;MQSB=0.128391;MQ0F=0	PL:DP:DV	0,57,255:19:0	0,24,221:8:0	0,27,223:9:0
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+X	3873	.	T	<*>	0	.	DP=35;I16=10,24,0,0,1242,46680,0,0,1852,104848,0,0,626,13428,0,0;QS=3,0;MQSB=0.0982034;MQ0F=0	PL:DP:DV	0,57,255:19:0	0,21,194:7:0	0,24,212:8:0
+X	3874	.	T	<*>	0	.	DP=36;I16=12,24,0,0,1290,47660,0,0,1972,112048,0,0,646,13774,0,0;QS=3,0;MQSB=0.182088;MQ0F=0	PL:DP:DV	0,60,255:20:0	0,24,228:8:0	0,24,204:8:0
+X	3875	.	T	<*>	0	.	DP=37;I16=13,24,0,0,1324,48418,0,0,2029,115297,0,0,657,14061,0,0;QS=3,0;MQSB=0.117872;MQ0F=0	PL:DP:DV	0,63,255:21:0	0,24,231:8:0	0,24,197:8:0
+X	3876	.	C	<*>	0	.	DP=37;I16=13,22,0,0,1248,45354,0,0,1909,108097,0,0,623,13325,0,0;QS=3,0;MQSB=0.140806;MQ0F=0	PL:DP:DV	0,60,255:20:0	0,21,196:7:0	0,24,180:8:0
+X	3877	.	C	<*>	0	.	DP=37;I16=13,24,0,0,1363,51201,0,0,2029,115297,0,0,681,14765,0,0;QS=3,0;MQSB=0.117872;MQ0F=0	PL:DP:DV	0,63,255:21:0	0,24,217:8:0	0,24,196:8:0
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+X	3912	.	A	C,<*>	0	.	DP=41;I16=17,22,0,1,1358,49508,16,256,2081,116491,60,3600,830,19358,11,121;QS=2.95181,0.0481928,0;SGB=-0.556633;RPB=1;MQB=1;MQSB=0.125266;BQB=1;MQ0F=0	PL:DP:DV	0,69,255,69,255,255:23:0	0,21,166,21,166,166:7:0	0,14,202,27,205,208:10:1
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+X	3914	.	T	<*>	0	.	DP=42;I16=16,24,0,0,1512,59342,0,0,2141,120091,0,0,823,19007,0,0;QS=3,0;MQSB=0.0846181;MQ0F=0	PL:DP:DV	0,69,255:23:0	0,21,192:7:0	0,30,228:10:0
+X	3915	.	C	<*>	0	.	DP=42;I16=16,24,0,0,1537,60953,0,0,2141,120091,0,0,799,18321,0,0;QS=3,0;MQSB=0.0846181;MQ0F=0	PL:DP:DV	0,72,255:24:0	0,18,176:6:0	0,30,229:10:0
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+X	3917	.	T	<*>	0	.	DP=43;I16=16,25,0,0,1601,65219,0,0,2201,123691,0,0,825,18875,0,0;QS=3,0;MQSB=0.0757469;MQ0F=0	PL:DP:DV	0,72,255:24:0	0,21,191:7:0	0,30,254:10:0
+X	3918	.	T	<*>	0	.	DP=43;I16=16,25,0,0,1541,60711,0,0,2201,123691,0,0,801,18239,0,0;QS=3,0;MQSB=0.0757469;MQ0F=0	PL:DP:DV	0,75,255:25:0	0,18,179:6:0	0,30,254:10:0
+X	3919	.	C	<*>	0	.	DP=42;I16=15,26,0,0,1621,66337,0,0,2232,126450,0,0,826,18786,0,0;QS=3,0;MQSB=0.110793;MQ0F=0	PL:DP:DV	0,72,255:24:0	0,21,200:7:0	0,30,242:10:0
+X	3920	.	T	<*>	0	.	DP=42;I16=15,26,0,0,1605,64327,0,0,2232,126450,0,0,825,18691,0,0;QS=3,0;MQSB=0.110793;MQ0F=0	PL:DP:DV	0,72,255:24:0	0,21,207:7:0	0,30,251:10:0
+X	3921	.	T	<*>	0	.	DP=42;I16=15,26,0,0,1519,58507,0,0,2232,126450,0,0,824,18630,0,0;QS=3,0;MQSB=0.110793;MQ0F=0	PL:DP:DV	0,72,255:24:0	0,21,201:7:0	0,30,242:10:0
+X	3922	.	A	<*>	0	.	DP=42;I16=14,26,0,0,1539,61289,0,0,2195,125081,0,0,819,18545,0,0;QS=3,0;MQSB=0.168991;MQ0F=0	PL:DP:DV	0,72,255:24:0	0,18,179:6:0	0,30,244:10:0
+X	3923	.	G	<*>	0	.	DP=41;I16=14,25,0,0,1515,60945,0,0,2135,121481,0,0,792,17834,0,0;QS=3,0;MQSB=0.182501;MQ0F=0	PL:DP:DV	0,69,255:23:0	0,18,172:6:0	0,30,240:10:0
+X	3924	.	G	<*>	0	.	DP=41;I16=13,26,0,0,1524,61106,0,0,2135,121481,0,0,808,18356,0,0;QS=3,0;MQSB=0.128469;MQ0F=0	PL:DP:DV	0,69,255:23:0	0,18,158:6:0	0,30,247:10:0
+X	3925	.	G	<*>	0	.	DP=41;I16=14,25,0,0,1425,55687,0,0,2135,121481,0,0,788,17758,0,0;QS=3,0;MQSB=0.182501;MQ0F=0	PL:DP:DV	0,72,255:24:0	0,15,134:5:0	0,30,245:10:0
+X	3926	.	C	<*>	0	.	DP=41;I16=14,26,0,0,1512,59674,0,0,2195,125081,0,0,811,18393,0,0;QS=3,0;MQSB=0.168991;MQ0F=0	PL:DP:DV	0,72,255:24:0	0,18,152:6:0	0,30,237:10:0
+X	3927	.	T	<*>	0	.	DP=41;I16=14,26,0,0,1512,59566,0,0,2195,125081,0,0,808,18384,0,0;QS=3,0;MQSB=0.168991;MQ0F=0	PL:DP:DV	0,72,255:24:0	0,18,160:6:0	0,30,237:10:0
+X	3928	.	G	<*>	0	.	DP=41;I16=14,25,0,0,1479,58495,0,0,2135,121481,0,0,779,17731,0,0;QS=3,0;MQSB=0.182501;MQ0F=0	PL:DP:DV	0,72,255:24:0	0,18,149:6:0	0,27,233:9:0
+X	3929	.	A	<*>	0	.	DP=41;I16=13,26,0,0,1452,56436,0,0,2135,121481,0,0,796,18256,0,0;QS=3,0;MQSB=0.128469;MQ0F=0	PL:DP:DV	0,69,255:23:0	0,18,161:6:0	0,30,220:10:0
+X	3930	.	T	<*>	0	.	DP=40;I16=13,25,0,0,1387,52929,0,0,2078,118232,0,0,767,17521,0,0;QS=3,0;MQSB=0.25797;MQ0F=0	PL:DP:DV	0,69,255:23:0	0,15,149:5:0	0,30,224:10:0
+X	3931	.	A	<*>	0	.	DP=40;I16=13,25,0,0,1387,52877,0,0,2078,118232,0,0,761,17439,0,0;QS=3,0;MQSB=0.25797;MQ0F=0	PL:DP:DV	0,69,255:23:0	0,18,166:6:0	0,27,222:9:0
+X	3932	.	T	<*>	0	.	DP=39;I16=12,26,0,0,1394,53644,0,0,2078,118232,0,0,780,17964,0,0;QS=3,0;MQSB=0.190372;MQ0F=0	PL:DP:DV	0,66,255:22:0	0,18,161:6:0	0,30,231:10:0
+X	3933	.	T	<*>	0	.	DP=38;I16=12,24,0,0,1389,54743,0,0,1958,111032,0,0,752,17366,0,0;QS=3,0;MQSB=0.218161;MQ0F=0	PL:DP:DV	0,66,255:22:0	0,18,166:6:0	0,24,220:8:0
+X	3934	.	C	<*>	0	.	DP=38;I16=12,25,0,0,1395,54915,0,0,2018,114632,0,0,768,17758,0,0;QS=3,0;MQSB=0.203497;MQ0F=0	PL:DP:DV	0,66,255:22:0	0,18,152:6:0	0,27,209:9:0
+X	3935	.	C	<*>	0	.	DP=38;I16=12,24,0,0,1239,44621,0,0,1958,111032,0,0,737,17075,0,0;QS=3,0;MQSB=0.218161;MQ0F=0	PL:DP:DV	0,66,255:22:0	0,15,134:5:0	0,27,170:9:0
+X	3936	.	A	G,<*>	0	.	DP=37;I16=5,6,6,17,424,16384,801,30271,609,34563,1314,77018,225,5325,511,11851;QS=0.87994,2.12006,0;VDB=0.0574114;SGB=-4.60123;RPB=0.741697;MQB=0.812605;MQSB=0.143788;BQB=0.883831;MQ0F=0	PL:DP:DV	233,0,206,255,239,255:20:11	77,0,58,83,70,141:6:4	196,24,0,196,24,196:8:8
+X	3937	.	C	<*>	0	.	DP=36;I16=11,24,0,0,1155,39875,0,0,1952,112422,0,0,745,17291,0,0;QS=3,0;MQSB=0.219636;MQ0F=0	PL:DP:DV	0,63,255:21:0	0,18,143:6:0	0,24,156:8:0
+X	3938	.	G	<*>	0	.	DP=35;I16=11,23,0,0,1155,41761,0,0,1892,108822,0,0,737,17079,0,0;QS=3,0;MQSB=0.231054;MQ0F=0	PL:DP:DV	0,63,255:21:0	0,15,119:5:0	0,24,176:8:0
+X	3939	.	C	<*>	0	.	DP=35;I16=11,22,0,0,1273,50651,0,0,1832,105222,0,0,703,16221,0,0;QS=3,0;MQSB=0.243713;MQ0F=0	PL:DP:DV	0,63,255:21:0	0,15,135:5:0	0,21,174:7:0
+X	3940	.	A	<*>	0	.	DP=35;I16=11,22,0,0,1148,42754,0,0,1832,105222,0,0,691,15867,0,0;QS=3,0;MQSB=0.243713;MQ0F=0	PL:DP:DV	0,63,255:21:0	0,15,117:5:0	0,21,163:7:0
+X	3941	.	C	<*>	0	.	DP=35;I16=11,22,0,0,1216,47488,0,0,1832,105222,0,0,688,15892,0,0;QS=3,0;MQSB=0.243713;MQ0F=0	PL:DP:DV	0,63,255:21:0	0,15,133:5:0	0,21,181:7:0
+X	3942	.	C	<*>	0	.	DP=35;I16=11,23,0,0,1336,54166,0,0,1892,108822,0,0,690,15772,0,0;QS=3,0;MQSB=0.231054;MQ0F=0	PL:DP:DV	0,63,255:21:0	0,15,140:5:0	0,24,195:8:0
+X	3943	.	T	<*>	0	.	DP=35;I16=11,23,0,0,1296,51618,0,0,1892,108822,0,0,676,15406,0,0;QS=3,0;MQSB=0.231054;MQ0F=0	PL:DP:DV	0,63,255:21:0	0,15,142:5:0	0,24,195:8:0
+X	3944	.	G	<*>	0	.	DP=34;I16=10,22,0,0,1199,46445,0,0,1803,104381,0,0,654,14954,0,0;QS=3,0;MQSB=0.1117;MQ0F=0	PL:DP:DV	0,57,255:19:0	0,15,149:5:0	0,24,195:8:0
+X	3945	.	C	<*>	0	.	DP=33;I16=10,22,0,0,1256,51226,0,0,1772,101622,0,0,649,14657,0,0;QS=3,0;MQSB=0.187579;MQ0F=0	PL:DP:DV	0,60,255:20:0	0,15,142:5:0	0,21,177:7:0
+X	3946	.	T	<*>	0	.	DP=33;I16=10,21,0,0,1170,45884,0,0,1712,98022,0,0,609,13599,0,0;QS=3,0;MQSB=0.199344;MQ0F=0	PL:DP:DV	0,60,255:20:0	0,15,144:5:0	0,18,158:6:0
+X	3947	.	A	<*>	0	.	DP=32;I16=10,21,0,0,1094,41048,0,0,1712,98022,0,0,620,13820,0,0;QS=3,0;MQSB=0.199344;MQ0F=0	PL:DP:DV	0,60,255:20:0	0,15,128:5:0	0,18,149:6:0
+X	3948	.	C	<*>	0	.	DP=32;I16=10,20,0,0,1134,45104,0,0,1652,94422,0,0,596,13344,0,0;QS=3,0;MQSB=0.212591;MQ0F=0	PL:DP:DV	0,60,255:20:0	0,12,105:4:0	0,18,155:6:0
+X	3949	.	A	C,<*>	0	.	DP=32;I16=10,17,0,1,1027,39909,24,576,1472,83622,60,3600,541,12211,25,625;QS=2.85093,0.149068,0;SGB=-0.556633;RPB=1;MQB=1;MQSB=0.244621;BQB=1;MQ0F=0	PL:DP:DV	0,60,255,60,255,255:20:0	0,9,89,9,89,89:3:0	9,0,107,21,110,124:5:1
+X	3950	.	C	<*>	0	.	DP=33;I16=11,21,0,0,1191,46247,0,0,1772,101622,0,0,576,12680,0,0;QS=3,0;MQSB=0.257801;MQ0F=0	PL:DP:DV	0,63,255:21:0	0,15,118:5:0	0,18,168:6:0
+X	3951	.	T	<*>	0	.	DP=34;I16=12,19,0,0,1148,44272,0,0,1712,98022,0,0,530,11670,0,0;QS=3,0;MQSB=0.354733;MQ0F=0	PL:DP:DV	0,63,255:21:0	0,15,146:5:0	0,15,152:5:0
+X	3952	.	C	<*>	0	.	DP=35;I16=13,20,0,0,1176,43762,0,0,1832,105222,0,0,545,12025,0,0;QS=3,0;MQSB=0.394875;MQ0F=0	PL:DP:DV	0,66,255:22:0	0,18,158:6:0	0,15,143:5:0
+X	3953	.	C	<*>	0	.	DP=34;I16=13,20,0,0,1246,48436,0,0,1863,107981,0,0,538,11772,0,0;QS=3,0;MQSB=0.252983;MQ0F=0	PL:DP:DV	0,63,255:21:0	0,18,163:6:0	0,18,168:6:0
+X	3954	.	T	<*>	0	.	DP=33;I16=13,19,0,0,1195,45815,0,0,1803,104381,0,0,526,11438,0,0;QS=3,0;MQSB=0.264585;MQ0F=0	PL:DP:DV	0,60,255:20:0	0,18,171:6:0	0,18,167:6:0
+X	3955	.	T	<*>	0	.	DP=32;I16=13,18,0,0,1180,46092,0,0,1743,100781,0,0,515,11139,0,0;QS=3,0;MQSB=0.277468;MQ0F=0	PL:DP:DV	0,57,255:19:0	0,18,173:6:0	0,18,174:6:0
+X	3956	.	C	<*>	0	.	DP=32;I16=13,18,0,0,1181,47021,0,0,1743,100781,0,0,504,10874,0,0;QS=3,0;MQSB=0.277468;MQ0F=0	PL:DP:DV	0,57,255:19:0	0,18,167:6:0	0,18,167:6:0
+X	3957	.	T	<*>	0	.	DP=31;I16=13,17,0,0,1153,46051,0,0,1683,97181,0,0,494,10642,0,0;QS=3,0;MQSB=0.291833;MQ0F=0	PL:DP:DV	0,57,255:19:0	0,18,161:6:0	0,15,162:5:0
+X	3958	.	T	<*>	0	.	DP=31;I16=13,16,0,0,1070,40600,0,0,1623,93581,0,0,483,10393,0,0;QS=3,0;MQSB=0.307929;MQ0F=0	PL:DP:DV	0,57,255:19:0	0,15,139:5:0	0,15,157:5:0
+X	3959	.	A	<*>	0	.	DP=30;I16=14,15,0,0,1062,39758,0,0,1623,93581,0,0,474,10176,0,0;QS=3,0;MQSB=0.377103;MQ0F=0	PL:DP:DV	0,60,255:20:0	0,12,118:4:0	0,15,154:5:0
+X	3960	.	T	<*>	0	.	DP=30;I16=14,15,0,0,995,36027,0,0,1623,93581,0,0,464,9892,0,0;QS=3,0;MQSB=0.377103;MQ0F=0	PL:DP:DV	0,60,255:20:0	0,12,105:4:0	0,15,142:5:0
+X	3961	.	G	<*>	0	.	DP=29;I16=12,16,0,0,1067,40899,0,0,1586,92212,0,0,457,9739,0,0;QS=3,0;MQSB=0.455864;MQ0F=0	PL:DP:DV	0,60,255:20:0	0,12,114:4:0	0,12,122:4:0
+X	3962	.	G	<*>	0	.	DP=29;I16=13,16,0,0,1025,37125,0,0,1623,93581,0,0,471,10053,0,0;QS=3,0;MQSB=0.307929;MQ0F=0	PL:DP:DV	0,60,255:20:0	0,12,108:4:0	0,15,144:5:0
+X	3963	.	C	<*>	0	.	DP=28;I16=13,15,0,0,1040,39100,0,0,1563,89981,0,0,463,9871,0,0;QS=3,0;MQSB=0.326055;MQ0F=0	PL:DP:DV	0,60,255:20:0	0,12,111:4:0	0,12,126:4:0
+X	3964	.	T	<*>	0	.	DP=27;I16=12,15,0,0,1036,39928,0,0,1503,86381,0,0,456,9720,0,0;QS=3,0;MQSB=0.273507;MQ0F=0	PL:DP:DV	0,60,255:20:0	0,9,94:3:0	0,12,133:4:0
+X	3965	.	G	<*>	0	.	DP=26;I16=12,14,0,0,993,38165,0,0,1443,82781,0,0,450,9598,0,0;QS=3,0;MQSB=0.29215;MQ0F=0	PL:DP:DV	0,57,255:19:0	0,9,92:3:0	0,12,134:4:0
+X	3966	.	A	<*>	0	.	DP=26;I16=12,13,0,0,930,34834,0,0,1406,81412,0,0,432,9310,0,0;QS=3,0;MQSB=0.520812;MQ0F=0	PL:DP:DV	0,54,255:18:0	0,9,90:3:0	0,12,140:4:0
+X	3967	.	T	<*>	0	.	DP=26;I16=12,13,0,0,900,32830,0,0,1406,81412,0,0,421,9001,0,0;QS=3,0;MQSB=0.520812;MQ0F=0	PL:DP:DV	0,57,255:19:0	0,9,90:3:0	0,9,100:3:0
+X	3968	.	A	<*>	0	.	DP=25;I16=12,13,0,0,885,31773,0,0,1406,81412,0,0,415,8853,0,0;QS=3,0;MQSB=0.520812;MQ0F=0	PL:DP:DV	0,57,255:19:0	0,9,90:3:0	0,9,99:3:0
+X	3969	.	T	<*>	0	.	DP=24;I16=11,13,0,0,886,32972,0,0,1369,80043,0,0,410,8736,0,0;QS=3,0;MQSB=0.702671;MQ0F=0	PL:DP:DV	0,54,255:18:0	0,9,85:3:0	0,9,108:3:0
+X	3970	.	T	<*>	0	.	DP=24;I16=11,13,0,0,861,31313,0,0,1369,80043,0,0,405,8649,0,0;QS=3,0;MQSB=0.702671;MQ0F=0	PL:DP:DV	0,54,255:18:0	0,9,83:3:0	0,9,104:3:0
+X	3971	.	C	<*>	0	.	DP=22;I16=11,11,0,0,815,30625,0,0,1249,72843,0,0,402,8590,0,0;QS=3,0;MQSB=0.751921;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,6,57:2:0	0,9,103:3:0
+X	3972	.	C	<*>	0	.	DP=22;I16=11,11,0,0,812,30486,0,0,1249,72843,0,0,399,8557,0,0;QS=3,0;MQSB=0.751921;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,6,55:2:0	0,9,96:3:0
+X	3973	.	A	<*>	0	.	DP=22;I16=11,11,0,0,795,28873,0,0,1249,72843,0,0,395,8501,0,0;QS=3,0;MQSB=0.751921;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,6,52:2:0	0,9,97:3:0
+X	3974	.	C	<*>	0	.	DP=22;I16=11,11,0,0,729,24447,0,0,1249,72843,0,0,392,8472,0,0;QS=3,0;MQSB=0.751921;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,6,55:2:0	0,9,78:3:0
+X	3975	.	G	<*>	0	.	DP=22;I16=11,11,0,0,717,24525,0,0,1249,72843,0,0,390,8470,0,0;QS=3,0;MQSB=0.751921;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,6,46:2:0	0,9,96:3:0
+X	3976	.	C	<*>	0	.	DP=22;I16=11,11,0,0,816,30652,0,0,1249,72843,0,0,387,8445,0,0;QS=3,0;MQSB=0.751921;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,6,55:2:0	0,9,97:3:0
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+X	4045	.	C	<*>	0	.	DP=10;I16=7,2,0,0,291,10099,0,0,494,27938,0,0,176,3906,0,0;QS=1,0;MQSB=0.714286;MQ0F=0	PL:DP:DV	0,27,204:9:0	0,0,0:0:0	0,0,0:0:0
+X	4046	.	C	<*>	0	.	DP=10;I16=8,2,0,0,356,13032,0,0,554,31538,0,0,177,3833,0,0;QS=2,0;MQSB=0.75;MQ0F=0	PL:DP:DV	0,27,212:9:0	0,3,35:1:0	0,0,0:0:0
+X	4047	.	A	<*>	0	.	DP=10;I16=8,2,0,0,347,12557,0,0,554,31538,0,0,172,3734,0,0;QS=2,0;MQSB=0.75;MQ0F=0	PL:DP:DV	0,27,204:9:0	0,3,40:1:0	0,0,0:0:0
+X	4048	.	C	<*>	0	.	DP=10;I16=8,2,0,0,342,12124,0,0,554,31538,0,0,167,3645,0,0;QS=2,0;MQSB=0.75;MQ0F=0	PL:DP:DV	0,27,202:9:0	0,3,37:1:0	0,0,0:0:0
+X	4049	.	G	<*>	0	.	DP=10;I16=7,2,0,0,260,7786,0,0,494,27938,0,0,146,3310,0,0;QS=2,0;MQSB=0.714286;MQ0F=0	PL:DP:DV	0,24,173:8:0	0,3,24:1:0	0,0,0:0:0
+X	4050	.	C	<*>	0	.	DP=9;I16=6,2,0,0,291,10813,0,0,434,24338,0,0,157,3495,0,0;QS=1,0;MQSB=0.666667;MQ0F=0	PL:DP:DV	0,24,204:8:0	0,0,0:0:0	0,0,0:0:0
+X	4051	.	A	<*>	0	.	DP=8;I16=5,2,0,0,259,9679,0,0,374,20738,0,0,146,3370,0,0;QS=1,0;MQSB=0.6;MQ0F=0	PL:DP:DV	0,21,192:7:0	0,0,0:0:0	0,0,0:0:0
+X	4052	.	C	<*>	0	.	DP=8;I16=5,2,0,0,247,9025,0,0,374,20738,0,0,143,3281,0,0;QS=1,0;MQSB=0.6;MQ0F=0	PL:DP:DV	0,21,190:7:0	0,0,0:0:0	0,0,0:0:0
+X	4053	.	C	<*>	0	.	DP=8;I16=6,2,0,0,254,9000,0,0,434,24338,0,0,146,3234,0,0;QS=1,0;MQSB=0.666667;MQ0F=0	PL:DP:DV	0,24,184:8:0	0,0,0:0:0	0,0,0:0:0
+X	4054	.	C	<*>	0	.	DP=8;I16=3,2,0,0,160,5344,0,0,254,13538,0,0,122,2984,0,0;QS=1,0;MQSB=0.333333;MQ0F=0	PL:DP:DV	0,15,134:5:0	0,0,0:0:0	0,0,0:0:0
+X	4055	.	G	<*>	0	.	DP=8;I16=6,2,0,0,230,6982,0,0,434,24338,0,0,138,3066,0,0;QS=1,0;MQSB=0.666667;MQ0F=0	PL:DP:DV	0,24,169:8:0	0,0,0:0:0	0,0,0:0:0
+X	4056	.	C	<*>	0	.	DP=8;I16=6,2,0,0,275,10153,0,0,434,24338,0,0,134,2994,0,0;QS=1,0;MQSB=0.666667;MQ0F=0	PL:DP:DV	0,24,197:8:0	0,0,0:0:0	0,0,0:0:0
+X	4057	.	T	<*>	0	.	DP=8;I16=5,2,0,0,243,8603,0,0,374,20738,0,0,127,2877,0,0;QS=1,0;MQSB=0.6;MQ0F=0	PL:DP:DV	0,21,182:7:0	0,0,0:0:0	0,0,0:0:0
+X	4058	.	A	<*>	0	.	DP=7;I16=4,2,0,0,214,7742,0,0,314,17138,0,0,116,2728,0,0;QS=1,0;MQSB=0.5;MQ0F=0	PL:DP:DV	0,18,171:6:0	0,0,0:0:0	0,0,0:0:0
+X	4059	.	C	<*>	0	.	DP=6;I16=4,2,0,0,204,7164,0,0,314,17138,0,0,119,2635,0,0;QS=1,0;MQSB=0.5;MQ0F=0	PL:DP:DV	0,18,168:6:0	0,0,0:0:0	0,0,0:0:0
+X	4060	.	A	<*>	0	.	DP=6;I16=4,2,0,0,227,8683,0,0,314,17138,0,0,115,2501,0,0;QS=1,0;MQSB=0.5;MQ0F=0	PL:DP:DV	0,18,177:6:0	0,0,0:0:0	0,0,0:0:0
+X	4061	.	C	<*>	0	.	DP=6;I16=4,2,0,0,193,6681,0,0,314,17138,0,0,111,2375,0,0;QS=1,0;MQSB=0.5;MQ0F=0	PL:DP:DV	0,18,157:6:0	0,0,0:0:0	0,0,0:0:0
+X	4062	.	T	<*>	0	.	DP=6;I16=4,1,0,0,195,7621,0,0,254,13538,0,0,82,1632,0,0;QS=1,0;MQSB=1;MQ0F=0	PL:DP:DV	0,15,151:5:0	0,0,0:0:0	0,0,0:0:0
+X	4063	.	C	<*>	0	.	DP=6;I16=4,2,0,0,216,7984,0,0,314,17138,0,0,102,2098,0,0;QS=1,0;MQSB=0.5;MQ0F=0	PL:DP:DV	0,18,170:6:0	0,0,0:0:0	0,0,0:0:0
+X	4064	.	C	<*>	0	.	DP=6;I16=4,2,0,0,227,8747,0,0,314,17138,0,0,97,1949,0,0;QS=1,0;MQSB=0.5;MQ0F=0	PL:DP:DV	0,18,177:6:0	0,0,0:0:0	0,0,0:0:0
+X	4065	.	T	<*>	0	.	DP=6;I16=4,2,0,0,202,6880,0,0,314,17138,0,0,92,1810,0,0;QS=1,0;MQSB=0.5;MQ0F=0	PL:DP:DV	0,18,161:6:0	0,0,0:0:0	0,0,0:0:0
+X	4066	.	T	<*>	0	.	DP=5;I16=3,2,0,0,180,6554,0,0,254,13538,0,0,88,1680,0,0;QS=1,0;MQSB=0.333333;MQ0F=0	PL:DP:DV	0,15,153:5:0	0,0,0:0:0	0,0,0:0:0
+X	4067	.	C	<*>	0	.	DP=5;I16=3,2,0,0,181,6637,0,0,254,13538,0,0,84,1558,0,0;QS=1,0;MQSB=0.333333;MQ0F=0	PL:DP:DV	0,15,153:5:0	0,0,0:0:0	0,0,0:0:0
+X	4068	.	T	<*>	0	.	DP=5;I16=3,2,0,0,198,7868,0,0,254,13538,0,0,80,1444,0,0;QS=1,0;MQSB=0.333333;MQ0F=0	PL:DP:DV	0,15,164:5:0	0,0,0:0:0	0,0,0:0:0
+X	4069	.	T	<*>	0	.	DP=5;I16=3,2,0,0,177,6325,0,0,254,13538,0,0,76,1338,0,0;QS=1,0;MQSB=0.333333;MQ0F=0	PL:DP:DV	0,15,154:5:0	0,0,0:0:0	0,0,0:0:0
+X	4070	.	A	<*>	0	.	DP=5;I16=3,2,0,0,161,5263,0,0,254,13538,0,0,72,1240,0,0;QS=1,0;MQSB=0.333333;MQ0F=0	PL:DP:DV	0,15,140:5:0	0,0,0:0:0	0,0,0:0:0
+X	4071	.	G	<*>	0	.	DP=5;I16=3,2,0,0,166,5658,0,0,254,13538,0,0,68,1150,0,0;QS=1,0;MQSB=0.333333;MQ0F=0	PL:DP:DV	0,15,142:5:0	0,0,0:0:0	0,0,0:0:0
+X	4072	.	G	<*>	0	.	DP=5;I16=2,2,0,0,138,4974,0,0,194,9938,0,0,55,987,0,0;QS=1,0;MQSB=0;MQ0F=0	PL:DP:DV	0,12,122:4:0	0,0,0:0:0	0,0,0:0:0
+X	4073	.	G	<*>	0	.	DP=5;I16=3,2,0,0,156,5082,0,0,254,13538,0,0,60,994,0,0;QS=1,0;MQSB=0.333333;MQ0F=0	PL:DP:DV	0,15,136:5:0	0,0,0:0:0	0,0,0:0:0
+X	4074	.	C	<*>	0	.	DP=5;I16=3,2,0,0,160,5602,0,0,254,13538,0,0,56,928,0,0;QS=1,0;MQSB=0.333333;MQ0F=0	PL:DP:DV	0,15,142:5:0	0,0,0:0:0	0,0,0:0:0
+X	4075	.	T	<*>	0	.	DP=5;I16=3,2,0,0,187,7069,0,0,254,13538,0,0,52,870,0,0;QS=1,0;MQSB=0.333333;MQ0F=0	PL:DP:DV	0,15,155:5:0	0,0,0:0:0	0,0,0:0:0
+X	4076	.	G	<*>	0	.	DP=5;I16=3,2,0,0,174,6298,0,0,254,13538,0,0,48,820,0,0;QS=1,0;MQSB=0.333333;MQ0F=0	PL:DP:DV	0,15,149:5:0	0,0,0:0:0	0,0,0:0:0
+X	4077	.	A	<*>	0	.	DP=4;I16=3,1,0,0,138,4810,0,0,194,9938,0,0,44,728,0,0;QS=1,0;MQSB=1;MQ0F=0	PL:DP:DV	0,12,121:4:0	0,0,0:0:0	0,0,0:0:0
+X	4078	.	T	<*>	0	.	DP=4;I16=3,1,0,0,143,5173,0,0,194,9938,0,0,40,644,0,0;QS=1,0;MQSB=1;MQ0F=0	PL:DP:DV	0,12,124:4:0	0,0,0:0:0	0,0,0:0:0
+X	4079	.	A	<*>	0	.	DP=4;I16=3,1,0,0,121,3847,0,0,194,9938,0,0,36,568,0,0;QS=1,0;MQSB=1;MQ0F=0	PL:DP:DV	0,12,107:4:0	0,0,0:0:0	0,0,0:0:0
+X	4080	.	T	<*>	0	.	DP=4;I16=3,0,0,0,106,3778,0,0,134,6338,0,0,25,451,0,0;QS=1,0;MQ0F=0	PL:DP:DV	0,9,87:3:0	0,0,0:0:0	0,0,0:0:0
+X	4081	.	T	<*>	0	.	DP=4;I16=3,1,0,0,106,2934,0,0,194,9938,0,0,28,440,0,0;QS=1,0;MQSB=1;MQ0F=0	PL:DP:DV	0,12,94:4:0	0,0,0:0:0	0,0,0:0:0
+X	4082	.	C	<*>	0	.	DP=3;I16=2,1,0,0,110,4042,0,0,134,6338,0,0,25,387,0,0;QS=1,0;MQSB=1;MQ0F=0	PL:DP:DV	0,9,103:3:0	0,0,0:0:0	0,0,0:0:0
+X	4083	.	C	<*>	0	.	DP=3;I16=2,1,0,0,104,3648,0,0,134,6338,0,0,22,340,0,0;QS=1,0;MQSB=1;MQ0F=0	PL:DP:DV	0,9,98:3:0	0,0,0:0:0	0,0,0:0:0
+X	4084	.	A	<*>	0	.	DP=2;I16=1,1,0,0,78,3050,0,0,97,4969,0,0,20,298,0,0;QS=1,0;MQSB=1;MQ0F=0	PL:DP:DV	0,6,74:2:0	0,0,0:0:0	0,0,0:0:0
+X	4085	.	C	<*>	0	.	DP=2;I16=1,1,0,0,62,1940,0,0,97,4969,0,0,18,260,0,0;QS=1,0;MQSB=1;MQ0F=0	PL:DP:DV	0,6,62:2:0	0,0,0:0:0	0,0,0:0:0
+X	4086	.	G	<*>	0	.	DP=2;I16=1,1,0,0,56,1640,0,0,97,4969,0,0,16,226,0,0;QS=1,0;MQSB=1;MQ0F=0	PL:DP:DV	0,6,56:2:0	0,0,0:0:0	0,0,0:0:0
+X	4087	.	C	<*>	0	.	DP=2;I16=1,1,0,0,69,2405,0,0,97,4969,0,0,14,196,0,0;QS=1,0;MQSB=1;MQ0F=0	PL:DP:DV	0,6,68:2:0	0,0,0:0:0	0,0,0:0:0
+X	4088	.	A	<*>	0	.	DP=1;I16=1,0,0,0,39,1521,0,0,37,1369,0,0,13,169,0,0;QS=1,0;MQ0F=0	PL:DP:DV	0,3,37:1:0	0,0,0:0:0	0,0,0:0:0
+X	4089	.	C	<*>	0	.	DP=1;I16=1,0,0,0,36,1296,0,0,37,1369,0,0,12,144,0,0;QS=1,0;MQ0F=0	PL:DP:DV	0,3,36:1:0	0,0,0:0:0	0,0,0:0:0
+X	4090	.	C	<*>	0	.	DP=1;I16=1,0,0,0,33,1089,0,0,37,1369,0,0,11,121,0,0;QS=1,0;MQ0F=0	PL:DP:DV	0,3,33:1:0	0,0,0:0:0	0,0,0:0:0
+X	4091	.	T	<*>	0	.	DP=1;I16=1,0,0,0,36,1296,0,0,37,1369,0,0,10,100,0,0;QS=1,0;MQ0F=0	PL:DP:DV	0,3,36:1:0	0,0,0:0:0	0,0,0:0:0
+X	4092	.	G	<*>	0	.	DP=1;I16=1,0,0,0,37,1369,0,0,37,1369,0,0,9,81,0,0;QS=1,0;MQ0F=0	PL:DP:DV	0,3,37:1:0	0,0,0:0:0	0,0,0:0:0
+X	4093	.	C	<*>	0	.	DP=1;I16=1,0,0,0,35,1225,0,0,37,1369,0,0,8,64,0,0;QS=1,0;MQ0F=0	PL:DP:DV	0,3,35:1:0	0,0,0:0:0	0,0,0:0:0
+X	4094	.	T	<*>	0	.	DP=1;I16=1,0,0,0,40,1600,0,0,37,1369,0,0,7,49,0,0;QS=1,0;MQ0F=0	PL:DP:DV	0,3,37:1:0	0,0,0:0:0	0,0,0:0:0
+X	4095	.	A	<*>	0	.	DP=1;I16=1,0,0,0,35,1225,0,0,37,1369,0,0,6,36,0,0;QS=1,0;MQ0F=0	PL:DP:DV	0,3,35:1:0	0,0,0:0:0	0,0,0:0:0
+X	4096	.	C	<*>	0	.	DP=1;I16=1,0,0,0,32,1024,0,0,37,1369,0,0,5,25,0,0;QS=1,0;MQ0F=0	PL:DP:DV	0,3,32:1:0	0,0,0:0:0	0,0,0:0:0
+X	4097	.	A	<*>	0	.	DP=1;I16=1,0,0,0,35,1225,0,0,37,1369,0,0,4,16,0,0;QS=1,0;MQ0F=0	PL:DP:DV	0,3,35:1:0	0,0,0:0:0	0,0,0:0:0
+X	4098	.	C	<*>	0	.	DP=1;I16=1,0,0,0,31,961,0,0,37,1369,0,0,3,9,0,0;QS=1,0;MQ0F=0	PL:DP:DV	0,3,31:1:0	0,0,0:0:0	0,0,0:0:0
+X	4099	.	T	<*>	0	.	DP=1;I16=1,0,0,0,32,1024,0,0,37,1369,0,0,2,4,0,0;QS=1,0;MQ0F=0	PL:DP:DV	0,3,32:1:0	0,0,0:0:0	0,0,0:0:0
+X	4100	.	C	<*>	0	.	DP=1;I16=1,0,0,0,27,729,0,0,37,1369,0,0,1,1,0,0;QS=1,0;MQ0F=0	PL:DP:DV	0,3,27:1:0	0,0,0:0:0	0,0,0:0:0
+X	4101	.	C	<*>	0	.	DP=1;I16=1,0,0,0,26,676,0,0,37,1369,0,0,0,0,0,0;QS=1,0;MQ0F=0	PL:DP:DV	0,3,26:1:0	0,0,0:0:0	0,0,0:0:0
diff --git a/test/mpileup.vcf b/test/mpileup.c.vcf
similarity index 100%
copy from test/mpileup.vcf
copy to test/mpileup.c.vcf
diff --git a/test/mpileup.cAls.out b/test/mpileup.cAls.out
index 660e7f5..105f294 100644
--- a/test/mpileup.cAls.out
+++ b/test/mpileup.cAls.out
@@ -27,6 +27,13 @@
 ##INFO=<ID=DP4,Number=4,Type=Integer,Description="Number of high-quality ref-forward , ref-reverse, alt-forward and alt-reverse bases">
 ##INFO=<ID=MQ,Number=1,Type=Integer,Description="Average mapping quality">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	HG00100	HG00101	HG00102
+17	1	.	A	G,T	0	.	DP=11;MQ0F=0;AC=0,0;AN=0;DP4=11,0,0,0;MQ=29	GT:PL:DP:DV	./.:0,0,0,0,0,0:5:0	./.:.:3:0	./.:.:3:0
+17	2	.	A	T,G	0	.	DP=11;MQ0F=0;AC=0,0;AN=0;DP4=11,0,0,0;MQ=29	GT:PL:DP:DV	./.:0,0,0,0,0,0:5:0	./.:.:3:0	./.:.:3:0
+17	3	.	A	C	0	.	DP=11;MQ0F=0;AC=0;AN=0;DP4=11,0,0,0;MQ=29	GT:PL:DP:DV	./.:0,0,0:5:0	./.:.:3:0	./.:.:3:0
+17	4	.	A	G,T,C	21.815	.	DP=11;MQ0F=0;AC=0,0,0;AN=2;DP4=11,0,0,0;MQ=29	GT:PL:DP:DV	0/0:1,2,3,7,8,10,11,12,14,15:5:0	./.:.:3:0	./.:.:3:0
+17	5	.	A	G,T	0	.	DP=11;MQ0F=0;AC=0,0;AN=0;DP4=11,0,0,0;MQ=29	GT:PL:DP:DV	./.:0,0,0,0,0,0:5:0	./.:.:3:0	./.:.:3:0
+17	6	.	A	T,G	0	.	DP=11;MQ0F=0;AC=0,0;AN=0;DP4=11,0,0,0;MQ=29	GT:PL:DP:DV	./.:0,0,0,0,0,0:5:0	./.:.:3:0	./.:.:3:0
+17	7	.	A	T,G,C	21.5769	.	DP=11;MQ0F=0;AC=0,0,0;AN=2;DP4=11,0,0,0;MQ=29	GT:PL:DP:DV	0/0:1,2,3,4,5,6,2,3,5,3:5:0	./.:.:3:0	./.:.:3:0
 17	828	.	T	C	409	.	DP=25;VDB=0.842082;SGB=-4.20907;RPB=0.950652;MQB=1;MQSB=1;BQB=0.929717;MQ0F=0;ICB=0.8;HOB=0.222222;AC=4;AN=6;DP4=2,4,8,11;MQ=60	GT:PL:DP:DV	0/1:211,0,35:12:10	0/1:116,0,91:9:5	1/1:120,12,0:4:4
 17	1665	.	T	C	3.10665	.	DP=20;VDB=0.1;SGB=0.346553;RPB=0.222222;MQB=0.611111;MQSB=0.988166;BQB=0.944444;MQ0F=0;ICB=0.128205;HOB=0.0555556;AC=1;AN=6;DP4=7,11,1,1;MQ=55	GT:PL:DP:DV	0/0:0,21,185:7:0	0/0:0,27,222:9:0	0/1:35,0,51:4:2
 17	2220	.	G	C	999	.	DP=21;VDB=0.532753;SGB=-3.51597;RPB=0.964198;MQB=0.898397;MQSB=0.875769;BQB=0.0354359;MQ0F=0;AC=0;AN=6;DP4=6,2,1,11;MQ=58	GT:PL:DP:DV	0/0:139,157,255:12:6	0/0:69,75,119:4:2	0/0:131,131,131:4:4
diff --git a/test/mpileup.ped b/test/mpileup.ped
new file mode 100644
index 0000000..c4226c6
--- /dev/null
+++ b/test/mpileup.ped
@@ -0,0 +1,3 @@
+HG00100 HG00100 0 0 2 0
+HG00101 HG00101 0 0 1 0
+HG00102 HG00102 0 0 2 0
diff --git a/test/mpileup.ploidy b/test/mpileup.ploidy
new file mode 100644
index 0000000..b9eba8a
--- /dev/null
+++ b/test/mpileup.ploidy
@@ -0,0 +1,4 @@
+X	1	1000	M	1
+X	3104	5000	M	1
+*	*	*	M	2
+*	*	*	F	2
diff --git a/test/mpileup.samples b/test/mpileup.samples
new file mode 100644
index 0000000..be818ea
--- /dev/null
+++ b/test/mpileup.samples
@@ -0,0 +1,3 @@
+HG00100	F
+HG00101	M
+HG00102	F
diff --git a/test/mpileup.tab b/test/mpileup.tab
index c585dad..1930ea0 100644
--- a/test/mpileup.tab
+++ b/test/mpileup.tab
@@ -1,3 +1,10 @@
+17	1	A,G,T
+17	2	A,T,G
+17	3	A,C
+17	4	A,C,T,G
+17	5	A,G,T
+17	6	A,T,G
+17	7	A,T,G,C
 17	828	T,C
 17	1665	T,C
 17	2220	G,C
diff --git a/test/mpileup.vcf b/test/mpileup.vcf
index 13c0132..155af1b 100644
--- a/test/mpileup.vcf
+++ b/test/mpileup.vcf
@@ -22,13 +22,13 @@
 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Number of high-quality bases">
 ##FORMAT=<ID=DV,Number=1,Type=Integer,Description="Number of high-quality non-reference bases">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	HG00100	HG00101	HG00102
-17	1	.	A	<X>	0	.	DP=11;I16=11,0,0,0,452,18594,0,0,319,9251,0,0,223,4959,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,72:3:0
-17	2	.	A	<X>	0	.	DP=11;I16=11,0,0,0,439,17587,0,0,319,9251,0,0,226,5030,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,72:3:0
-17	3	.	G	<X>	0	.	DP=11;I16=11,0,0,0,431,16971,0,0,319,9251,0,0,229,5111,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,72:3:0
-17	4	.	C	<X>	0	.	DP=11;I16=11,0,0,0,423,16417,0,0,319,9251,0,0,232,5202,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,71:3:0
-17	5	.	T	<X>	0	.	DP=11;I16=11,0,0,0,450,18520,0,0,319,9251,0,0,234,5252,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,72:3:0
-17	6	.	T	<X>	0	.	DP=11;I16=11,0,0,0,403,14847,0,0,319,9251,0,0,236,5310,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,72:3:0
-17	7	.	C	<X>	0	.	DP=11;I16=11,0,0,0,446,18114,0,0,319,9251,0,0,237,5327,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,72:3:0
+17	1	.	A	G,X,T,C	0	.	DP=11;I16=11,0,0,0,452,18594,0,0,319,9251,0,0,223,4959,0,0;QS=1,1,0,1,1;MQ0F=0	PL:DP:DV	0,0,0,0,0,0,.,.,.,.,.,.,.,.,.:5:0	.:3:0	.:3:0
+17	2	.	A	G,X,T,C	0	.	DP=11;I16=11,0,0,0,452,18594,0,0,319,9251,0,0,223,4959,0,0;QS=1,1,0,1,1;MQ0F=0	PL:DP:DV	0,0,0,0,0,0,.,.,.,.,.,.,.,.,.:5:0	.:3:0	.:3:0
+17	3	.	A	G,X,T,C	0	.	DP=11;I16=11,0,0,0,452,18594,0,0,319,9251,0,0,223,4959,0,0;QS=1,1,0,1,1;MQ0F=0	PL:DP:DV	0,0,0,0,0,0,.,.,.,.,.,.,.,.,.:5:0	.:3:0	.:3:0
+17	4	.	A	G,X,T,C	0	.	DP=11;I16=11,0,0,0,452,18594,0,0,319,9251,0,0,223,4959,0,0;QS=1,1,0,1,1;MQ0F=0	PL:DP:DV	1,2,3,4,5,6,7,8,9,10,11,12,13,14,15:5:0	.:3:0	.:3:0
+17	5	.	A	X,G	0	.	DP=11;I16=11,0,0,0,452,18594,0,0,319,9251,0,0,223,4959,0,0;QS=1,0,1;MQ0F=0	PL:DP:DV	0,0,0,0,0,0:5:0	.:3:0	.:3:0
+17	6	.	A	X,G	0	.	DP=11;I16=11,0,0,0,452,18594,0,0,319,9251,0,0,223,4959,0,0;QS=1,0,1;MQ0F=0	PL:DP:DV	0,0,0,0,0,0:5:0	.:3:0	.:3:0
+17	7	.	A	X,G	0	.	DP=11;I16=11,0,0,0,452,18594,0,0,319,9251,0,0,223,4959,0,0;QS=1,0,1;MQ0F=0	PL:DP:DV	1,2,3,4,5,6:5:0	.:3:0	.:3:0
 17	8	.	T	<X>	0	.	DP=11;I16=11,0,0,0,465,19677,0,0,319,9251,0,0,238,5354,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,72:3:0
 17	9	.	C	<X>	0	.	DP=11;I16=11,0,0,0,447,18205,0,0,319,9251,0,0,239,5391,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,72:3:0
 17	10	.	A	<X>	0	.	DP=11;I16=11,0,0,0,426,16756,0,0,319,9251,0,0,240,5438,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,69:3:0
diff --git a/test/norm.fa b/test/norm.fa
index 2ef85f1..53e6b16 100644
--- a/test/norm.fa
+++ b/test/norm.fa
@@ -22,3 +22,5 @@ ACTGGACACGTGGACACACACACACACACACACACACACACAGTCAAACCACCTACCAGA
 TCCCCTCTTGACCTCTCTCTATTTTTTTTTTTTTTTCTGAGATGGATTTTTGCTCTTGTT
 >5 20:18724313-18724343
 GTCTCAAAAAAAAAAAAAAAAAAAAGAAAAG
+>21
+TTTATTATTATTATTATTAAATTGAATTTATTTAGTGTACATACATTCATGTGTATTGTG
diff --git a/test/norm.fa.fai b/test/norm.fa.fai
index 72d2ebe..40b06b7 100644
--- a/test/norm.fa.fai
+++ b/test/norm.fa.fai
@@ -4,3 +4,4 @@
 3	60	902	60	61
 4	60	985	60	61
 5	31	1070	31	32
+21	60	1106	60	61
diff --git a/test/norm.merge.2.out b/test/norm.merge.2.out
new file mode 100644
index 0000000..d3c1414
--- /dev/null
+++ b/test/norm.merge.2.out
@@ -0,0 +1,38 @@
+##fileformat=VCFv4.1
+##FILTER=<ID=PASS,Description="All filters passed">
+##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Phred-scaled likelihood">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Depth">
+##contig=<ID=1,length=2147483647>
+##contig=<ID=2,length=2147483647>
+##contig=<ID=20,length=2147483647>
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
+##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##INFO=<ID=XRF,Number=R,Type=Float,Description="Test Number=AGR in INFO">
+##INFO=<ID=XAF,Number=A,Type=Float,Description="Test Number=AGR in INFO">
+##INFO=<ID=XGF,Number=G,Type=Float,Description="Test Number=AGR in INFO">
+##INFO=<ID=XRI,Number=R,Type=Integer,Description="Test Number=AGR in INFO">
+##INFO=<ID=XAI,Number=A,Type=Integer,Description="Test Number=AGR in INFO">
+##INFO=<ID=XGI,Number=G,Type=Integer,Description="Test Number=AGR in INFO">
+##INFO=<ID=XRS,Number=R,Type=String,Description="Test Number=AGR in INFO">
+##INFO=<ID=XAS,Number=A,Type=String,Description="Test Number=AGR in INFO">
+##INFO=<ID=XGS,Number=G,Type=String,Description="Test Number=AGR in INFO">
+##FORMAT=<ID=FRF,Number=R,Type=Float,Description="Test Number=AGR in FORMAT">
+##FORMAT=<ID=FAF,Number=A,Type=Float,Description="Test Number=AGR in FORMAT">
+##FORMAT=<ID=FGF,Number=G,Type=Float,Description="Test Number=AGR in FORMAT">
+##FORMAT=<ID=FRI,Number=R,Type=Integer,Description="Test Number=AGR in FORMAT">
+##FORMAT=<ID=FAI,Number=A,Type=Integer,Description="Test Number=AGR in FORMAT">
+##FORMAT=<ID=FGI,Number=G,Type=Integer,Description="Test Number=AGR in FORMAT">
+##FORMAT=<ID=FRS,Number=R,Type=String,Description="Test Number=AGR in FORMAT">
+##FORMAT=<ID=FAS,Number=A,Type=String,Description="Test Number=AGR in FORMAT">
+##FORMAT=<ID=FGS,Number=G,Type=String,Description="Test Number=AGR in FORMAT">
+##FORMAT=<ID=FSTR,Number=1,Type=String,Description="Test String in FORMAT">
+##INFO=<ID=ISTR,Number=1,Type=String,Description="Test String in INFO">
+##FILTER=<ID=FAIL1,Description="Failed filter 1">
+##FILTER=<ID=FAIL2,Description="Failed filter 2">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	XY00001	XY00002	XY00003
+1	105	.	T	C	999	PASS	.	GT:FGI:FRI	1:1,2:3,4	0/1:5,6,7:8,9	0/1:.:.,.
+1	110	.	C	A	999	PASS	.	GT:FGI	1:1,2	0:3,4	0:.
+1	150	.	A	C	999	PASS	.	GT:FGI	1:1,2	0:.	0:3,4
diff --git a/test/norm.merge.2.vcf b/test/norm.merge.2.vcf
new file mode 100644
index 0000000..779551a
--- /dev/null
+++ b/test/norm.merge.2.vcf
@@ -0,0 +1,41 @@
+##fileformat=VCFv4.1
+##FILTER=<ID=PASS,Description="All filters passed">
+##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Phred-scaled likelihood">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Depth">
+##contig=<ID=1,length=2147483647>
+##contig=<ID=2,length=2147483647>
+##contig=<ID=20,length=2147483647>
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
+##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##INFO=<ID=XRF,Number=R,Type=Float,Description="Test Number=AGR in INFO">
+##INFO=<ID=XAF,Number=A,Type=Float,Description="Test Number=AGR in INFO">
+##INFO=<ID=XGF,Number=G,Type=Float,Description="Test Number=AGR in INFO">
+##INFO=<ID=XRI,Number=R,Type=Integer,Description="Test Number=AGR in INFO">
+##INFO=<ID=XAI,Number=A,Type=Integer,Description="Test Number=AGR in INFO">
+##INFO=<ID=XGI,Number=G,Type=Integer,Description="Test Number=AGR in INFO">
+##INFO=<ID=XRS,Number=R,Type=String,Description="Test Number=AGR in INFO">
+##INFO=<ID=XAS,Number=A,Type=String,Description="Test Number=AGR in INFO">
+##INFO=<ID=XGS,Number=G,Type=String,Description="Test Number=AGR in INFO">
+##FORMAT=<ID=FRF,Number=R,Type=Float,Description="Test Number=AGR in FORMAT">
+##FORMAT=<ID=FAF,Number=A,Type=Float,Description="Test Number=AGR in FORMAT">
+##FORMAT=<ID=FGF,Number=G,Type=Float,Description="Test Number=AGR in FORMAT">
+##FORMAT=<ID=FRI,Number=R,Type=Integer,Description="Test Number=AGR in FORMAT">
+##FORMAT=<ID=FAI,Number=A,Type=Integer,Description="Test Number=AGR in FORMAT">
+##FORMAT=<ID=FGI,Number=G,Type=Integer,Description="Test Number=AGR in FORMAT">
+##FORMAT=<ID=FRS,Number=R,Type=String,Description="Test Number=AGR in FORMAT">
+##FORMAT=<ID=FAS,Number=A,Type=String,Description="Test Number=AGR in FORMAT">
+##FORMAT=<ID=FGS,Number=G,Type=String,Description="Test Number=AGR in FORMAT">
+##FORMAT=<ID=FSTR,Number=1,Type=String,Description="Test String in FORMAT">
+##INFO=<ID=ISTR,Number=1,Type=String,Description="Test String in INFO">
+##FILTER=<ID=FAIL1,Description="Failed filter 1">
+##FILTER=<ID=FAIL2,Description="Failed filter 2">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	XY00001	XY00002	XY00003
+1	105	.	T	.	999	PASS	.	GT:FGI:FRI	0:.:.	0/0:.:.	0/1:.:.
+1	105	.	T	C	999	PASS	.	GT:FGI:FRI	1:1,2:3,4	0/1:5,6,7:8,9	0/1:.:.
+1	110	.	C	.	999	PASS	.	GT:FGI	0:.	0:.	0:.
+1	110	.	C	A	999	PASS	.	GT:FGI	1:1,2	0:3,4	0:.
+1	150	.	A	.	999	PASS	.	GT:FGI	0:.	0:.	0:.
+1	150	.	A	C	999	PASS	.	GT:FGI	1:1,2	0:.	0:3,4
diff --git a/test/norm.merge.3.out b/test/norm.merge.3.out
new file mode 100644
index 0000000..788a427
--- /dev/null
+++ b/test/norm.merge.3.out
@@ -0,0 +1,34 @@
+##fileformat=VCFv4.2
+##FILTER=<ID=PASS,Description="All filters passed">
+##contig=<ID=11,length=2147483647>
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=FL,Number=1,Type=Float,Description="Float">
+##FORMAT=<ID=FLG,Number=G,Type=Float,Description="FloatG">
+##FORMAT=<ID=FLA,Number=A,Type=Float,Description="FloatA">
+##FORMAT=<ID=FLR,Number=R,Type=Float,Description="FloatR">
+##FORMAT=<ID=INT,Number=1,Type=Float,Description="Int">
+##FORMAT=<ID=INTG,Number=G,Type=Float,Description="IntG">
+##FORMAT=<ID=INTA,Number=A,Type=Integer,Description="IntA">
+##FORMAT=<ID=INTR,Number=R,Type=Integer,Description="IntR">
+##FORMAT=<ID=ST,Number=1,Type=String,Description="String">
+##FORMAT=<ID=STA,Number=A,Type=String,Description="StringA">
+##FORMAT=<ID=STR,Number=R,Type=String,Description="StringR">
+##FORMAT=<ID=STG,Number=G,Type=String,Description="StringG">
+##INFO=<ID=FL,Number=1,Type=Float,Description="Float">
+##INFO=<ID=FLG,Number=G,Type=Float,Description="FloatG">
+##INFO=<ID=FLA,Number=A,Type=Float,Description="FloatA">
+##INFO=<ID=FLR,Number=R,Type=Float,Description="FloatR">
+##INFO=<ID=INT,Number=1,Type=Float,Description="Int">
+##INFO=<ID=INTG,Number=G,Type=Float,Description="IntG">
+##INFO=<ID=INTA,Number=A,Type=Integer,Description="IntA">
+##INFO=<ID=INTR,Number=R,Type=Integer,Description="IntR">
+##INFO=<ID=F1,Type=Flag,Description="Flag1">
+##INFO=<ID=ST,Number=1,Type=String,Description="String">
+##INFO=<ID=STA,Number=A,Type=String,Description="StringA">
+##INFO=<ID=STR,Number=R,Type=String,Description="StringR">
+##INFO=<ID=STG,Number=G,Type=String,Description="StringG">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	sample_1	sample_2
+11	48245184	.	C	G	.	PASS	FL=0.34;FLG=0.1,0,0.9;FLA=88.4;FLR=99,88.4;INT=0;INTG=0,1,9;INTA=88;INTR=99,88;F1;ST=alpha;STA=alpha;STR=alpha,beta;STG=alpha,beta,gamma	GT:FL:FLG:FLA:FLR:INT:INTG:INTA:INTR:ST:STA:STR:STG	0|0:0.34:0.1,0,0.9:88.4:99,88.4:0:0,1,9:88:99,88:alpha:alpha:alpha,beta:alpha,beta,gamma	0|0:0.34:0.1,0,0.9:88.4:99,88.4:0:0,1,9:88:99,88:alpha:alpha:alpha,beta:alpha,beta,gamma
+11	48245185	.	C	G,T	.	PASS	FL=0.34;FLG=0.1,0,0.9,.,.,.;FLA=88.4,.;FLR=99,88.4,.;INT=0;INTG=0,1,9,.,.,.;INTA=88,.;INTR=99,88,.;F1;ST=alpha;STA=alpha,.;STR=alpha,beta,.;STG=alpha,beta,gamma,.,.,.	GT:FL:FLG:FLA:FLR:INT:INTG:INTA:INTR:ST:STA:STR:STG	0|0:0.34:0.1,0,0.9,.,.,.:88.4,.:99,88.4,.:0:0,1,9,.,.,.:88,.:99,88,.:alpha:alpha,.:alpha,beta,.:alpha,beta,gamma,.,.,.	0|0:0.34:0.1,0,0.9,.,.,.:88.4,.:99,88.4,.:0:0,1,9,.,.,.:88,.:99,88,.:alpha:alpha,.:alpha,beta,.:alpha,beta,gamma,.,.,.
+11	48245186	.	C	G,T	.	PASS	FL=0.34;FLA=88.4,88.4;FLR=99,88.4,88.4;INT=0;INTA=88,11;INTR=99,88,11;F1;ST=alpha;STA=alpha,beta;STR=alpha,beta,gamma	GT:FL:FLA:FLR:INT:INTA:INTR:ST:STA:STR	0|0:0.34:88.4,11:99,88.4,11:0:88,11:99,88,11:alpha:alpha,beta:alpha,beta,gamma	0|0:0.34:88.4,11:99,88.4,11:0:88,11:99,88,11:alpha:alpha,beta:alpha,beta,gamma
+11	48245187	.	C	G,T	.	PASS	FL=0.34;FLA=88.4,.;FLR=99,88.4,.;INT=0;INTA=88,.;INTR=99,88,.;F1;ST=alpha;STA=alpha,.;STR=alpha,beta,.	GT:FL:FLG:FLA:FLR:INT:INTG:INTA:INTR:ST:STA:STR:STG	0:0.34:0.1,0,.:88.4,.:99,88.4,.:0:0,1,.:88,.:99,88,.:alpha:alpha,.:alpha,beta,.:alpha,beta,.	0:0.34:0.1,0,.:88.4,.:99,88.4,.:0:0,1,.:88,.:99,88,.:alpha:alpha,.:alpha,beta,.:alpha,beta,.
diff --git a/test/norm.merge.3.vcf b/test/norm.merge.3.vcf
new file mode 100644
index 0000000..f2b980a
--- /dev/null
+++ b/test/norm.merge.3.vcf
@@ -0,0 +1,37 @@
+##fileformat=VCFv4.2
+##contig=<ID=11,length=2147483647>
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=FL,Number=1,Type=Float,Description="Float">
+##FORMAT=<ID=FLG,Number=G,Type=Float,Description="FloatG">
+##FORMAT=<ID=FLA,Number=A,Type=Float,Description="FloatA">
+##FORMAT=<ID=FLR,Number=R,Type=Float,Description="FloatR">
+##FORMAT=<ID=INT,Number=1,Type=Float,Description="Int">
+##FORMAT=<ID=INTG,Number=G,Type=Float,Description="IntG">
+##FORMAT=<ID=INTA,Number=A,Type=Integer,Description="IntA">
+##FORMAT=<ID=INTR,Number=R,Type=Integer,Description="IntR">
+##FORMAT=<ID=ST,Number=1,Type=String,Description="String">
+##FORMAT=<ID=STA,Number=A,Type=String,Description="StringA">
+##FORMAT=<ID=STR,Number=R,Type=String,Description="StringR">
+##FORMAT=<ID=STG,Number=G,Type=String,Description="StringG">
+##INFO=<ID=FL,Number=1,Type=Float,Description="Float">
+##INFO=<ID=FLG,Number=G,Type=Float,Description="FloatG">
+##INFO=<ID=FLA,Number=A,Type=Float,Description="FloatA">
+##INFO=<ID=FLR,Number=R,Type=Float,Description="FloatR">
+##INFO=<ID=INT,Number=1,Type=Float,Description="Int">
+##INFO=<ID=INTG,Number=G,Type=Float,Description="IntG">
+##INFO=<ID=INTA,Number=A,Type=Integer,Description="IntA">
+##INFO=<ID=INTR,Number=R,Type=Integer,Description="IntR">
+##INFO=<ID=F1,Type=Flag,Description="Flag1">
+##INFO=<ID=ST,Number=1,Type=String,Description="String">
+##INFO=<ID=STA,Number=A,Type=String,Description="StringA">
+##INFO=<ID=STR,Number=R,Type=String,Description="StringR">
+##INFO=<ID=STG,Number=G,Type=String,Description="StringG">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	sample_1	sample_2
+11	48245184	.	C	G	.	PASS	FL=0.34;FLG=0.1,0,0.9;FLA=88.4;FLR=99.0,88.4;INT=0;INTG=0,1,9;INTA=88;INTR=99,88;F1;ST=alpha;STA=alpha;STR=alpha,beta;STG=alpha,beta,gamma	GT:FL:FLG:FLA:FLR:INT:INTG:INTA:INTR:ST:STA:STR:STG	0|0:0.34:0.1,0,0.9:88.4:99.0,88.4:0:0,1,9:88:99,88:alpha:alpha:alpha,beta:alpha,beta,gamma	0|0:0.34:0.1,0,0.9:88.4:99.0,88.4:0:0,1,9:88:99,88:alpha:alpha:alpha,beta:alpha,beta,gamma
+11	48245184	.	C	G	.	PASS	.	GT	0/0	0/0
+11	48245185	.	C	G	.	PASS	FL=0.34;FLG=0.1,0,0.9;FLA=88.4;FLR=99.0,88.4;INT=0;INTG=0,1,9;INTA=88;INTR=99,88;F1;ST=alpha;STA=alpha;STR=alpha,beta;STG=alpha,beta,gamma	GT:FL:FLG:FLA:FLR:INT:INTG:INTA:INTR:ST:STA:STR:STG	0|0:0.34:0.1,0,0.9:88.4:99.0,88.4:0:0,1,9:88:99,88:alpha:alpha:alpha,beta:alpha,beta,gamma	0|0:0.34:0.1,0,0.9:88.4:99.0,88.4:0:0,1,9:88:99,88:alpha:alpha:alpha,beta:alpha,beta,gamma
+11	48245185	.	C	T	.	PASS	.	GT	0/0	0/0
+11	48245186	.	C	G,T	.	PASS	FL=0.34;FLA=88.4,88.4;FLR=99.0,88.4,88.4;INT=0;INTA=88,11;INTR=99,88,11;F1;ST=alpha;STA=alpha,beta;STR=alpha,beta,gamma	GT:FL:FLA:FLR:INT:INTA:INTR:ST:STA:STR	0|0:0.34:88.4,11:99.0,88.4,11:0:88,11:99,88,11:alpha:alpha,beta:alpha,beta,gamma	0|0:0.34:88.4,11:99.0,88.4,11:0:88,11:99,88,11:alpha:alpha,beta:alpha,beta,gamma
+11	48245186	.	C	T	.	PASS	.	GT	0/0	0/0
+11	48245187	.	C	G	.	PASS	FL=0.34;FLA=88.4;FLR=99.0,88.4;INT=0;INTA=88;INTR=99,88;F1;ST=alpha;STA=alpha;STR=alpha,beta	GT:FL:FLG:FLA:FLR:INT:INTG:INTA:INTR:ST:STA:STR:STG	0:0.34:0.1,0:88.4:99.0,88.4:0:0,1:88:99,88:alpha:alpha:alpha,beta:alpha,beta	0:0.34:0.1,0:88.4:99.0,88.4:0:0,1:88:99,88:alpha:alpha:alpha,beta:alpha,beta
+11	48245187	.	C	T	.	PASS	.	GT	0	0
diff --git a/test/norm.merge.out b/test/norm.merge.out
index 6dd3f31..f5b1092 100644
--- a/test/norm.merge.out
+++ b/test/norm.merge.out
@@ -1,4 +1,4 @@
-##fileformat=VCFv4.1
+##fileformat=VCFv4.2
 ##FILTER=<ID=PASS,Description="All filters passed">
 ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
diff --git a/test/norm.merge.strict.out b/test/norm.merge.strict.out
index c24dc9b..1395d22 100644
--- a/test/norm.merge.strict.out
+++ b/test/norm.merge.strict.out
@@ -1,4 +1,4 @@
-##fileformat=VCFv4.1
+##fileformat=VCFv4.2
 ##FILTER=<ID=PASS,Description="All filters passed">
 ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
diff --git a/test/norm.merge.vcf b/test/norm.merge.vcf
index a24e36f..e89178e 100644
--- a/test/norm.merge.vcf
+++ b/test/norm.merge.vcf
@@ -1,4 +1,4 @@
-##fileformat=VCFv4.1
+##fileformat=VCFv4.2
 ##FILTER=<ID=PASS,Description="All filters passed">
 ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
diff --git a/test/norm.out b/test/norm.out
index 6db87c1..e6796d1 100644
--- a/test/norm.out
+++ b/test/norm.out
@@ -1,4 +1,4 @@
-##fileformat=VCFv4.1
+##fileformat=VCFv4.2
 ##FILTER=<ID=PASS,Description="All filters passed">
 ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
diff --git a/test/norm.setref.out b/test/norm.setref.out
new file mode 100644
index 0000000..2856b0a
--- /dev/null
+++ b/test/norm.setref.out
@@ -0,0 +1,45 @@
+##fileformat=VCFv4.2
+##FILTER=<ID=PASS,Description="All filters passed">
+##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Phred-scaled likelihood">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Depth">
+##contig=<ID=1,length=2147483647>
+##contig=<ID=2,length=2147483647>
+##contig=<ID=3,length=2147483647>
+##contig=<ID=4,length=2147483647>
+##contig=<ID=5,length=2147483647>
+##contig=<ID=20,length=2147483647>
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
+##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##INFO=<ID=XRF,Number=R,Type=Float,Description="Test Number=AGR in INFO">
+##INFO=<ID=XAF,Number=A,Type=Float,Description="Test Number=AGR in INFO">
+##INFO=<ID=XGF,Number=G,Type=Float,Description="Test Number=AGR in INFO">
+##INFO=<ID=XRI,Number=R,Type=Integer,Description="Test Number=AGR in INFO">
+##INFO=<ID=XAI,Number=A,Type=Integer,Description="Test Number=AGR in INFO">
+##INFO=<ID=XGI,Number=G,Type=Integer,Description="Test Number=AGR in INFO">
+##INFO=<ID=XRS,Number=R,Type=String,Description="Test Number=AGR in INFO">
+##INFO=<ID=XAS,Number=A,Type=String,Description="Test Number=AGR in INFO">
+##INFO=<ID=XGS,Number=G,Type=String,Description="Test Number=AGR in INFO">
+##FORMAT=<ID=FRF,Number=R,Type=Float,Description="Test Number=AGR in FORMAT">
+##FORMAT=<ID=FAF,Number=A,Type=Float,Description="Test Number=AGR in FORMAT">
+##FORMAT=<ID=FGF,Number=G,Type=Float,Description="Test Number=AGR in FORMAT">
+##FORMAT=<ID=FRI,Number=R,Type=Integer,Description="Test Number=AGR in FORMAT">
+##FORMAT=<ID=FAI,Number=A,Type=Integer,Description="Test Number=AGR in FORMAT">
+##FORMAT=<ID=FGI,Number=G,Type=Integer,Description="Test Number=AGR in FORMAT">
+##FORMAT=<ID=FRS,Number=R,Type=String,Description="Test Number=AGR in FORMAT">
+##FORMAT=<ID=FAS,Number=A,Type=String,Description="Test Number=AGR in FORMAT">
+##FORMAT=<ID=FGS,Number=G,Type=String,Description="Test Number=AGR in FORMAT">
+##FORMAT=<ID=FSTR,Number=1,Type=String,Description="Test String in FORMAT">
+##INFO=<ID=ISTR,Number=1,Type=String,Description="Test String in INFO">
+##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	XY00001	XY00002
+1	105	.	TAAACCCTAAA	TAACCCTAAA,TAA	999	PASS	INDEL;AN=4;AC=0,2;DP=19	GT	0/2	0/2
+2	101	.	A	c	999	PASS	INDEL;AN=4;AC=4	GT:DP	1/1:1	1/1:1
+2	105	.	T	<DEL>	999	PASS	END=112;AN=4;AC=3	GT:DP	0/1:1	1/1:1
+2	115	.	c	t	999	PASS	INDEL;AN=4;AC=0	GT:DP	0/0:1	0/0:1
+20	3	.	g	c	999	PASS	INDEL;AN=4;AC=3	GT	1/1	1/0
+20	3	.	gatg	gact	999	PASS	INDEL;AN=4;AC=2	GT	0/1	0/1
+20	10	.	C	.	999	PASS	INDEL;AN=4;AC=1	GT	1/0	0/0
+20	275	.	a	c,g,t,aaa	999	PASS	INDEL;AN=2;AC=0,0,0,0	GT	0	0
diff --git a/test/norm.setref.vcf b/test/norm.setref.vcf
new file mode 100644
index 0000000..da78f10
--- /dev/null
+++ b/test/norm.setref.vcf
@@ -0,0 +1,45 @@
+##fileformat=VCFv4.2
+##FILTER=<ID=PASS,Description="All filters passed">
+##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Phred-scaled likelihood">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Depth">
+##contig=<ID=1,length=2147483647>
+##contig=<ID=2,length=2147483647>
+##contig=<ID=3,length=2147483647>
+##contig=<ID=4,length=2147483647>
+##contig=<ID=5,length=2147483647>
+##contig=<ID=20,length=2147483647>
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
+##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##INFO=<ID=XRF,Number=R,Type=Float,Description="Test Number=AGR in INFO">
+##INFO=<ID=XAF,Number=A,Type=Float,Description="Test Number=AGR in INFO">
+##INFO=<ID=XGF,Number=G,Type=Float,Description="Test Number=AGR in INFO">
+##INFO=<ID=XRI,Number=R,Type=Integer,Description="Test Number=AGR in INFO">
+##INFO=<ID=XAI,Number=A,Type=Integer,Description="Test Number=AGR in INFO">
+##INFO=<ID=XGI,Number=G,Type=Integer,Description="Test Number=AGR in INFO">
+##INFO=<ID=XRS,Number=R,Type=String,Description="Test Number=AGR in INFO">
+##INFO=<ID=XAS,Number=A,Type=String,Description="Test Number=AGR in INFO">
+##INFO=<ID=XGS,Number=G,Type=String,Description="Test Number=AGR in INFO">
+##FORMAT=<ID=FRF,Number=R,Type=Float,Description="Test Number=AGR in FORMAT">
+##FORMAT=<ID=FAF,Number=A,Type=Float,Description="Test Number=AGR in FORMAT">
+##FORMAT=<ID=FGF,Number=G,Type=Float,Description="Test Number=AGR in FORMAT">
+##FORMAT=<ID=FRI,Number=R,Type=Integer,Description="Test Number=AGR in FORMAT">
+##FORMAT=<ID=FAI,Number=A,Type=Integer,Description="Test Number=AGR in FORMAT">
+##FORMAT=<ID=FGI,Number=G,Type=Integer,Description="Test Number=AGR in FORMAT">
+##FORMAT=<ID=FRS,Number=R,Type=String,Description="Test Number=AGR in FORMAT">
+##FORMAT=<ID=FAS,Number=A,Type=String,Description="Test Number=AGR in FORMAT">
+##FORMAT=<ID=FGS,Number=G,Type=String,Description="Test Number=AGR in FORMAT">
+##FORMAT=<ID=FSTR,Number=1,Type=String,Description="Test String in FORMAT">
+##INFO=<ID=ISTR,Number=1,Type=String,Description="Test String in INFO">
+##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	XY00001	XY00002
+1	105	.	TAACCCTAAA	TAAACCCTAAA,TAA	999	PASS	INDEL;AN=4;AC=2,2;DP=19	GT	1/2	1/2
+2	101	.	.	c	999	PASS	INDEL;AN=4;AC=4	GT:DP	1/1:1	1/1:1
+2	105	.	n	<DEL>	999	PASS	END=112;AN=4;AC=3	GT:DP	0/1:1	1/1:1
+2	115	.	t	c	999	PASS	INDEL;AN=4;AC=4	GT:DP	1/1:1	1/1:1
+20	3	.	c	g	999	PASS	INDEL;AN=4;AC=1	GT	0/0	0/1
+20	3	.	gact	gatg	999	PASS	INDEL;AN=4;AC=2	GT	1/0	1/0
+20	10	.	.	.	999	PASS	INDEL;AN=4;AC=1	GT	1/0	0/0
+20	275	.	g	c,a,t,aaa	999	PASS	INDEL;AN=2;AC=0,2,0,0	GT	2	2
diff --git a/test/norm.split.2.out b/test/norm.split.2.out
new file mode 100644
index 0000000..52fcecd
--- /dev/null
+++ b/test/norm.split.2.out
@@ -0,0 +1,107 @@
+##fileformat=VCFv4.2
+##FILTER=<ID=PASS,Description="All filters passed">
+##samtoolsVersion=1.2-216-gdffc67f-dirty+htslib-1.2.1-216-gd2ed7e6-dirty
+##reference=file:///usr/bio-ref/GRCh38.81/GRCh38.fa
+##contig=<ID=1,length=248956422>
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
+1	789241	.	C	G	41.4503	.	.
+1	789262	.	G	A	36.0809	.	.
+1	789280	.	T	C	40.0265	.	.
+1	789334	.	A	T	67	.	.
+1	789348	.	T	A	44.5622	.	.
+1	789368	.	A	T	18.5381	.	.
+1	789369	.	C	T	30.0396	.	.
+1	789396	.	A	C	35.7056	.	.
+1	789402	.	G	T	35.0554	.	.
+1	789403	.	T	A	35.0681	.	.
+1	789417	.	T	G	35.0681	.	.
+1	789420	.	T	A	35.0681	.	.
+1	789429	.	A	C	39.1119	.	.
+1	789435	.	C	T	35.1179	.	.
+1	789481	.	G	A	94	.	.
+1	789489	.	C	A	89	.	.
+1	789491	.	C	G	100	.	.
+1	789568	.	TATGGAATGGAATGGAATGGAATG	TATGGAATGGAATGGAATG	295	.	.
+1	789631	.	G	A	3.18972	.	.
+1	789642	.	T	G	3.66362	.	.
+1	789660	.	C	T	35.0294	.	.
+1	789666	.	T	G	16.1313	.	.
+1	789673	.	A	T	52	.	.
+1	789675	.	T	G	20.7408	.	.
+1	789676	.	C	T	26.6621	.	.
+1	789680	.	A	T	21.5713	.	.
+1	789680	.	AGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGACTCGAATGGAATGGAATGGAATG	AGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGACTCGAATGGAATGGAATGGAATG	23.495	.	.
+1	789685	.	T	G	6.53871	.	.
+1	789690	.	T	G	16.2287	.	.
+1	789690	.	T	C	16.2287	.	.
+1	789691	.	G	T	21.8633	.	.
+1	789691	.	G	C	21.8633	.	.
+1	789692	.	G	A	31.8203	.	.
+1	789695	.	T	A	7.03922	.	.
+1	789696	.	G	A	64	.	.
+1	789696	.	G	T	64	.	.
+1	789696	.	G	C	64	.	.
+1	789697	.	G	A	116	.	.
+1	789700	.	T	A	27.3447	.	.
+1	789700	.	T	G	27.3447	.	.
+1	789704	.	A	C	12.9378	.	.
+1	789704	.	A	T	12.9378	.	.
+1	789704	.	A	G	12.9378	.	.
+1	789706	.	G	C	4.49441	.	.
+1	789706	.	G	A	4.49441	.	.
+1	789707	.	G	C	6.28796	.	.
+1	789707	.	G	A	6.28796	.	.
+1	789710	.	T	G	59	.	.
+1	789710	.	T	A	59	.	.
+1	789711	.	G	T	15.1544	.	.
+1	789713	.	A	C	6.69714	.	.
+1	789717	.	G	A	82	.	.
+1	789720	.	T	G	26.241	.	.
+1	789721	.	G	A	99	.	.
+1	789721	.	G	T	99	.	.
+1	789727	.	G	A	5.18898	.	.
+1	789727	.	G	C	5.18898	.	.
+1	789730	.	T	A	73	.	.
+1	789730	.	T	C	73	.	.
+1	789731	.	G	T	111	.	.
+1	789732	.	G	T	24.8095	.	.
+1	789735	.	T	G	61	.	.
+1	789737	.	G	T	69	.	.
+1	789737	.	G	A	69	.	.
+1	789739	.	A	T	48.5355	.	.
+1	789740	.	T	A	29.8166	.	.
+1	789747	.	A	G	187	.	.
+1	789747	.	A	C	187	.	.
+1	789747	.	A	T	187	.	.
+1	789749	.	C	G	19.1565	.	.
+1	789750	.	T	A	12.5086	.	.
+1	789750	.	T	C	12.5086	.	.
+1	789752	.	C	G	284	.	.
+1	789757	.	G	A	7.13117	.	.
+1	789765	.	T	A	191	.	.
+1	789767	.	G	A	16.2222	.	.
+1	789769	.	C	T	17.4827	.	.
+1	789770	.	T	G	64	.	.
+1	789770	.	T	A	64	.	.
+1	789772	.	G	A	31.6793	.	.
+1	789772	.	G	C	31.6793	.	.
+1	789775	.	T	A	125	.	.
+1	789775	.	T	G	125	.	.
+1	789776	.	A	G	151	.	.
+1	789777	.	G	C	22.9639	.	.
+1	789781	.	G	A	89	.	.
+1	789795	.	A	T	11.555	.	.
+1	789816	.	G	A	29.3537	.	.
+1	789957	.	C	G	19.4796	.	.
+1	790009	.	C	T	55	.	.
+1	790136	.	A	G	85	.	.
+1	790156	.	G	A	19.4198	.	.
+1	790176	.	A	G	86	.	.
+1	790179	.	C	T	4.20807	.	.
+1	790181	.	C	T	12.5149	.	.
+1	790186	.	G	A	86	.	.
+1	790189	.	T	A	76	.	.
+1	790202	.	G	A	86	.	.
+1	790202	.	G	C	86	.	.
+1	790206	.	C	A	18.4041	.	.
+1	790206	.	C	T	18.4041	.	.
diff --git a/test/norm.split.2.vcf b/test/norm.split.2.vcf
new file mode 100644
index 0000000..b8147fc
--- /dev/null
+++ b/test/norm.split.2.vcf
@@ -0,0 +1,85 @@
+##fileformat=VCFv4.2
+##FILTER=<ID=PASS,Description="All filters passed">
+##samtoolsVersion=1.2-216-gdffc67f-dirty+htslib-1.2.1-216-gd2ed7e6-dirty
+##reference=file:///usr/bio-ref/GRCh38.81/GRCh38.fa
+##contig=<ID=1,length=248956422>
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER
+1	789241	.	C	G	41.4503	.
+1	789262	.	G	A	36.0809	.
+1	789280	.	T	C	40.0265	.
+1	789334	.	A	T	67	.
+1	789348	.	T	A	44.5622	.
+1	789368	.	A	T	18.5381	.
+1	789369	.	C	T	30.0396	.
+1	789396	.	A	C	35.7056	.
+1	789402	.	G	T	35.0554	.
+1	789403	.	T	A	35.0681	.
+1	789417	.	T	G	35.0681	.
+1	789420	.	T	A	35.0681	.
+1	789429	.	A	C	39.1119	.
+1	789435	.	C	T	35.1179	.
+1	789481	.	G	A	94	.
+1	789489	.	C	A	89	.
+1	789491	.	C	G	100	.
+1	789568	.	TATGGAATGGAATGGAATGGAATG	TATGGAATGGAATGGAATG	295	.
+1	789631	.	G	A	3.18972	.
+1	789642	.	T	G	3.66362	.
+1	789660	.	C	T	35.0294	.
+1	789666	.	T	G	16.1313	.
+1	789673	.	A	T	52	.
+1	789675	.	T	G	20.7408	.
+1	789676	.	C	T	26.6621	.
+1	789680	.	A	T	21.5713	.
+1	789680	.	AGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGACTCGAATGGAATGGAATGGAATG	AGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGACTCGAATGGAATGGAATGGAATG	23.495	.
+1	789685	.	T	G	6.53871	.
+1	789690	.	T	G,C	16.2287	.
+1	789691	.	G	T,C	21.8633	.
+1	789692	.	G	A	31.8203	.
+1	789695	.	T	A	7.03922	.
+1	789696	.	G	A,T,C	64	.
+1	789697	.	G	A	116	.
+1	789700	.	T	A,G	27.3447	.
+1	789704	.	A	C,T,G	12.9378	.
+1	789706	.	G	C,A	4.49441	.
+1	789707	.	G	C,A	6.28796	.
+1	789710	.	T	G,A	59	.
+1	789711	.	G	T	15.1544	.
+1	789713	.	A	C	6.69714	.
+1	789717	.	G	A	82	.
+1	789720	.	T	G	26.241	.
+1	789721	.	G	A,T	99	.
+1	789727	.	G	A,C	5.18898	.
+1	789730	.	T	A,C	73	.
+1	789731	.	G	T	111	.
+1	789732	.	G	T	24.8095	.
+1	789735	.	T	G	61	.
+1	789737	.	G	T,A	69	.
+1	789739	.	A	T	48.5355	.
+1	789740	.	T	A	29.8166	.
+1	789747	.	A	G,C,T	187	.
+1	789749	.	C	G	19.1565	.
+1	789750	.	T	A,C	12.5086	.
+1	789752	.	C	G	284	.
+1	789757	.	G	A	7.13117	.
+1	789765	.	T	A	191	.
+1	789767	.	G	A	16.2222	.
+1	789769	.	C	T	17.4827	.
+1	789770	.	T	G,A	64	.
+1	789772	.	G	A,C	31.6793	.
+1	789775	.	T	A,G	125	.
+1	789776	.	A	G	151	.
+1	789777	.	G	C	22.9639	.
+1	789781	.	G	A	89	.
+1	789795	.	A	T	11.555	.
+1	789816	.	G	A	29.3537	.
+1	789957	.	C	G	19.4796	.
+1	790009	.	C	T	55	.
+1	790136	.	A	G	85	.
+1	790156	.	G	A	19.4198	.
+1	790176	.	A	G	86	.
+1	790179	.	C	T	4.20807	.
+1	790181	.	C	T	12.5149	.
+1	790186	.	G	A	86	.
+1	790189	.	T	A	76	.
+1	790202	.	G	A,C	86	.
+1	790206	.	C	A,T	18.4041	.
\ No newline at end of file
diff --git a/test/norm.out b/test/norm.split.and.norm.out
similarity index 60%
copy from test/norm.out
copy to test/norm.split.and.norm.out
index 6db87c1..64838ed 100644
--- a/test/norm.out
+++ b/test/norm.split.and.norm.out
@@ -1,4 +1,4 @@
-##fileformat=VCFv4.1
+##fileformat=VCFv4.2
 ##FILTER=<ID=PASS,Description="All filters passed">
 ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
@@ -6,10 +6,8 @@
 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Depth">
 ##contig=<ID=1,length=2147483647>
 ##contig=<ID=2,length=2147483647>
-##contig=<ID=3,length=2147483647>
-##contig=<ID=4,length=2147483647>
-##contig=<ID=5,length=2147483647>
 ##contig=<ID=20,length=2147483647>
+##contig=<ID=21,length=2147483647>
 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes">
 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
@@ -34,24 +32,33 @@
 ##FORMAT=<ID=FSTR,Number=1,Type=String,Description="Test String in FORMAT">
 ##INFO=<ID=ISTR,Number=1,Type=String,Description="Test String in INFO">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	XY00001	XY00002
-1	105	.	TAAACCCTA	T,TAACCCTA	999	PASS	INDEL;AN=4;AC=2,2;DP=19;ISTR=SomeString;XRF=1e+06,2e+06,500000;XRI=1111,2222,5555;XRS=AAA,BBB,DDD;XAF=1e+06,500000;XAI=1111,5555;XAS=AAA,DDD;XGF=1e+06,2e+06,3e+06,500000,.,9e+09;XGI=1111,2222,3333,5555,.,9999;XGS=A,B,C,E,.,F	GT:PL:DP:FRF:FRI:FRS:FAF:FAI:FAS:FGF:FGI:FGS	1/2:1,2,3,4,5,6:1:1e+06,2e+06,500000:1111,2222,5555:AAAA,BBB,CC:1e+06,500000:1111,5555:A,BB:1e+06,2e+06,3e+06,500000,.,9e+09:1111,2222,3333,5555,.,9999:A,BB,CCC,EEEE,.,FFFFF	1/2:1,2,3, [...]
+1	105	.	TAAACCCTA	T	999	PASS	INDEL;AN=4;AC=2;DP=19;ISTR=SomeString;XRF=1e+06,2e+06;XRI=1111,2222;XRS=AAA,BBB;XAF=1e+06;XAI=1111;XAS=AAA;XGF=1e+06,2e+06,3e+06;XGI=1111,2222,3333;XGS=A,B,C	GT:PL:DP:FRF:FRI:FRS:FAF:FAI:FAS:FGF:FGI:FGS	1/0:1,2,3:1:1e+06,2e+06:1111,2222:AAAA,BBB:1e+06:1111:A:1e+06,2e+06,3e+06:1111,2222,3333:A,BB,CCC	1/0:1,2,3:1:1e+06,2e+06:1111,2222:AAAA,BBB:1e+06:1111:A:1e+06,2e+06,3e+06:1111,2222,3333:A,BB,CCC
+1	105	.	TA	T	999	PASS	INDEL;AN=4;AC=2;DP=19;ISTR=SomeString;XRF=1e+06,500000;XRI=1111,5555;XRS=AAA,DDD;XAF=500000;XAI=5555;XAS=DDD;XGF=1e+06,500000,9e+09;XGI=1111,5555,9999;XGS=A,E,F	GT:PL:DP:FRF:FRI:FRS:FAF:FAI:FAS:FGF:FGI:FGS	0/1:1,4,6:1:1e+06,500000:1111,5555:AAAA,CC:500000:5555:BB:1e+06,500000,9e+09:1111,5555,9999:A,EEEE,FFFFF	0/1:1,4,6:1:1e+06,500000:1111,5555:AAAA,CC:500000:5555:BB:1e+06,500000,9e+09:1111,5555,9999:A,EEEE,FFFFF
 2	1	.	GGGCGTCTCATAGCTGGAGCAATGGCGAGCGCCTGGACAAGGGAGGGGAAGGGGTTCTTATTACTGACGCGGGTAGCCCCTACTGCTGTGTGGTTCCCCTATTTTTTTTTTTTTCTTTTTGAGACGGAGTCTCGCTCTGTCACCCAGGCTGGAGTGCAGTGGCACAATCTCGGCTCACTGCAAGCTCCACC	ACG	999	PASS	INDEL;AN=4;AC=2	GT:DP	1/0:1	1/0:1
 2	101	.	A	ATT	999	PASS	INDEL;AN=4;AC=4	GT:DP	1/1:1	1/1:1
-2	114	.	T	TTC,TT	999	PASS	INDEL;AN=4;AC=2,2	GT:DP	1/2:1	1/2:1
+2	101	.	A	AT	999	PASS	INDEL;AN=4;AC=2	GT:DP	0/1:1	0/1:1
+2	114	.	T	TTC	999	PASS	INDEL;AN=4;AC=2	GT:DP	1/0:1	1/0:1
 2	115	.	C	T	999	PASS	INDEL;AN=4;AC=4	GT:DP	1/1:1	1/1:1
 20	3	.	G	CT	999	PASS	INDEL;AN=4;AC=2	GT	0/1	0/1
 20	5	.	TG	CT	999	PASS	INDEL;AN=4;AC=2	GT	1/0	1/0
-20	5	.	TGGG	TAC,TG,TGGGG,AC	.	PASS	INDEL;AN=4;AC=2,2,0,0	GT:PL:DP	1/2:1,2,3,4,5,6,7,8,9,10,11,12,13,14,15:1	1/2:1,2,3,4,5,6,7,8,9,10,11,12,13,14,15:1
+20	5	.	TGG	T	.	PASS	INDEL;AN=4;AC=2	GT:PL:DP	0/1:1,4,6:1	0/1:1,4,6:1
+20	5	.	T	TG	.	PASS	INDEL;AN=4;AC=0	GT:PL:DP	0/0:1,7,10:1	0/0:1,7,10:1
+20	5	.	TGGG	AC	.	PASS	INDEL;AN=4;AC=0	GT:PL:DP	0/0:1,11,15:1	0/0:1,11,15:1
+20	6	.	GGG	AC	.	PASS	INDEL;AN=4;AC=2	GT:PL:DP	1/0:1,2,3:1	1/0:1,2,3:1
 20	59	.	AG	.	999	PASS	AN=4	GT:PL:DP	0/0:0:4	0/0:0:4
 20	81	.	A	C	999	PASS	AN=4;AC=2	GT:PL:DP	0/1:255,0,255:13	0/1:255,0,255:13
 20	84	.	G	T	999	PASS	AN=4;AC=2	GT:PL:DP	0/1:255,0,255:13	0/1:255,0,255:13
 20	95	.	T	A	999	PASS	AN=4;AC=2	GT:PL:DP	0/1:255,0,255:13	0/1:255,0,255:13
 20	95	.	TCACCG	AAAAAA	999	PASS	AN=4;AC=2	GT:PL:DP	0/1:255,0,255:13	0/1:255,0,255:13
-20	273	.	C	CAA,CAAA	999	PASS	INDEL;AN=4;AC=2,2	GT:PL:DP	1/2:0,3,5,3,5,5:1	1/2:0,3,5,3,5,5:1
+20	273	.	C	CAA	999	PASS	INDEL;AN=4;AC=2	GT:PL:DP	1/0:0,3,5:1	1/0:0,3,5:1
+20	273	.	C	CAAA	999	PASS	INDEL;AN=4;AC=2	GT:PL:DP	0/1:0,3,5:1	0/1:0,3,5:1
 20	273	.	C	CAAAAAAAAAA	999	PASS	INDEL;AN=0;AC=0	GT:PL:DP	./.:0,0,0:0	./.:0,0,0:0
 20	273	.	C	CAA	999	PASS	INDEL;AN=0;AC=0	GT:PL:DP	./.:0,0,0:0	./.:0,0,0:0
-20	275	.	A	C,G	999	PASS	INDEL;AN=2;AC=0,2	GT:PL:DP:FGF:FGI:FGS:FSTR	2:0,0,0:0:1e+06,2e+06,3e+06:1111,2222,3333:A,BB,CCC:WORD	2:0,0,0:0:1e+06,2e+06,3e+06:1111,2222,3333:A,BB,CCC:WORD
-3	10	.	GTGGAC	GTGGACACAC,GTGGACAC,GTGGACACACAC,GTGG,GTGGACACACACAC,ATGGACACACAC	999	PASS	INDEL;AN=0	GT:DP	./.:0	./.:0
-3	17	.	CA	C	999	PASS	INDEL;AN=0	GT:DP	./.:0	./.:0
-4	36	.	TC	C,TT,TTC	999	PASS	INDEL;AN=0	GT:DP	./.:0	./.:0
-5	21	.	A	AAG	999	PASS	INDEL;AN=0	GT:DP	./.:0	./.:0
+20	275	.	A	C	999	PASS	INDEL;AN=2;AC=0	GT:PL:DP:FGF:FGI:FGS:FSTR	0:0,0:0:1e+06,2e+06:1111,2222:A,BB:WORD	0:0,0:0:1e+06,2e+06:1111,2222:A,BB:WORD
+20	275	.	A	G	999	PASS	INDEL;AN=2;AC=2	GT:PL:DP:FGF:FGI:FGS:FSTR	1:0,0:0:1e+06,3e+06:1111,3333:A,CCC:WORD	1:0,0:0:1e+06,3e+06:1111,3333:A,CCC:WORD
+20	300	.	T	C	999	PASS	INDEL;AN=0;AC=0	GT:PL:DP	./.:0,0,0:0	./.:0,0,0:0
+20	300	.	T	G	999	PASS	INDEL;AN=0;AC=0	GT:PL:DP	./.:0,0,0:0	./.:0,0,0:0
+21	1	id	T	TTTATTA	999	PASS	INDEL;AN=0;AC=0	GT:DP	./.:0	./.:0
+21	1	id	T	TTTATTATTATTATTATTA	999	PASS	INDEL;AN=0;AC=0	GT:DP	./.:0	./.:0
+21	1	id	TTTA	T	999	PASS	INDEL;AN=0;AC=0	GT:DP	./.:0	./.:0
+21	1	id	T	TTATTA	999	PASS	INDEL;AN=0;AC=0	GT:DP	./.:0	./.:0
diff --git a/test/norm.split.out b/test/norm.split.out
index cf70808..b919211 100644
--- a/test/norm.split.out
+++ b/test/norm.split.out
@@ -1,4 +1,4 @@
-##fileformat=VCFv4.1
+##fileformat=VCFv4.2
 ##FILTER=<ID=PASS,Description="All filters passed">
 ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
@@ -7,6 +7,7 @@
 ##contig=<ID=1,length=2147483647>
 ##contig=<ID=2,length=2147483647>
 ##contig=<ID=20,length=2147483647>
+##contig=<ID=21,length=2147483647>
 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes">
 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
@@ -55,5 +56,9 @@
 20	275	.	A	C	999	PASS	INDEL;AN=2;AC=0	GT:PL:DP:FGF:FGI:FGS:FSTR	0:0,0:0:1e+06,2e+06:1111,2222:A,BB:WORD	0:0,0:0:1e+06,2e+06:1111,2222:A,BB:WORD
 20	275	.	A	G	999	PASS	INDEL;AN=2;AC=2	GT:PL:DP:FGF:FGI:FGS:FSTR	1:0,0:0:1e+06,3e+06:1111,3333:A,CCC:WORD	1:0,0:0:1e+06,3e+06:1111,3333:A,CCC:WORD
 20	278	.	AAAAAAAAAAAAAAAAA	AAAAAAAAAAAAAAAAAAA	999	PASS	INDEL;AN=0;AC=0	GT:PL:DP	./.:0,0,0:0	./.:0,0,0:0
-20	300	.	A	C	999	PASS	INDEL;AN=0;AC=0	GT:PL:DP	./.:0,0,0:0	./.:0,0,0:0
-20	300	.	A	G	999	PASS	INDEL;AN=0;AC=0	GT:PL:DP	./.:0,0,0:0	./.:0,0,0:0
+20	300	.	T	C	999	PASS	INDEL;AN=0;AC=0	GT:PL:DP	./.:0,0,0:0	./.:0,0,0:0
+20	300	.	T	G	999	PASS	INDEL;AN=0;AC=0	GT:PL:DP	./.:0,0,0:0	./.:0,0,0:0
+21	1	id	TTTA	TTTATTATTA	999	PASS	INDEL;AN=0;AC=0	GT:DP	./.:0	./.:0
+21	1	id	TTTA	TTTATTATTATTATTATTATTA	999	PASS	INDEL;AN=0;AC=0	GT:DP	./.:0	./.:0
+21	1	id	TTTA	T	999	PASS	INDEL;AN=0;AC=0	GT:DP	./.:0	./.:0
+21	1	id	TTTA	TTATTATTA	999	PASS	INDEL;AN=0;AC=0	GT:DP	./.:0	./.:0
diff --git a/test/norm.split.vcf b/test/norm.split.vcf
index 6e55d18..7f039d1 100644
--- a/test/norm.split.vcf
+++ b/test/norm.split.vcf
@@ -1,4 +1,4 @@
-##fileformat=VCFv4.1
+##fileformat=VCFv4.2
 ##FILTER=<ID=PASS,Description="All filters passed">
 ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
@@ -7,6 +7,7 @@
 ##contig=<ID=1,length=2147483647>
 ##contig=<ID=2,length=2147483647>
 ##contig=<ID=20,length=2147483647>
+##contig=<ID=21,length=2147483647>
 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes">
 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
@@ -48,4 +49,5 @@
 20	274	.	AAAAAAAAA	AAAAAAAAAAAAAAAAAAA	999	PASS	INDEL;AN=0;AC=0	GT:PL:DP	./.:0,0,0:0	./.:0,0,0:0
 20	275	.	A	C,G	999	PASS	INDEL;AN=2;AC=0,2	GT:PL:DP:FGF:FGI:FGS:FSTR	2:0,0,0:0:1e+06,2e+06,3e+06:1111,2222,3333:A,BB,CCC:WORD	2:0,0,0:0:1e+06,2e+06,3e+06:1111,2222,3333:A,BB,CCC:WORD
 20	278	.	AAAAAAAAAAAAAAAAA	AAAAAAAAAAAAAAAAAAA	999	PASS	INDEL;AN=0;AC=0	GT:PL:DP	./.:0,0,0:0	./.:0,0,0:0
-20	300	.	A	C,G	999	PASS	INDEL;AN=0;AC=0,0	GT:PL:DP	./.:0,0,0,0,0,0:0	./.:0,0,0,0,0,0:0
+20	300	.	T	C,G	999	PASS	INDEL;AN=0;AC=0,0	GT:PL:DP	./.:0,0,0,0,0,0:0	./.:0,0,0,0,0,0:0
+21	1	id	TTTA	TTTATTATTA,TTTATTATTATTATTATTATTA,T,TTATTATTA	999	PASS	INDEL;AN=0;AC=0,0,0,0	GT:DP	./.:0	./.:0
diff --git a/test/norm.vcf b/test/norm.vcf
index 52f5f88..d000655 100644
--- a/test/norm.vcf
+++ b/test/norm.vcf
@@ -1,4 +1,4 @@
-##fileformat=VCFv4.1
+##fileformat=VCFv4.2
 ##FILTER=<ID=PASS,Description="All filters passed">
 ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
diff --git a/test/query.18.out b/test/query.18.out
new file mode 100644
index 0000000..9618498
--- /dev/null
+++ b/test/query.18.out
@@ -0,0 +1,2 @@
+3000002 .
+3000003 .
diff --git a/test/query.19.out b/test/query.19.out
new file mode 100644
index 0000000..f16b4ab
--- /dev/null
+++ b/test/query.19.out
@@ -0,0 +1,3 @@
+3000001 11
+3000004 11
+3000005 1
diff --git a/test/query.20.out b/test/query.20.out
new file mode 100644
index 0000000..9618498
--- /dev/null
+++ b/test/query.20.out
@@ -0,0 +1,2 @@
+3000002 .
+3000003 .
diff --git a/test/query.21.out b/test/query.21.out
new file mode 100644
index 0000000..ead31a1
--- /dev/null
+++ b/test/query.21.out
@@ -0,0 +1,3 @@
+3000001 1.1
+3000004 1.1
+3000005 1
diff --git a/test/query.22.out b/test/query.22.out
new file mode 100644
index 0000000..9618498
--- /dev/null
+++ b/test/query.22.out
@@ -0,0 +1,2 @@
+3000002 .
+3000003 .
diff --git a/test/query.23.out b/test/query.23.out
new file mode 100644
index 0000000..3594a84
--- /dev/null
+++ b/test/query.23.out
@@ -0,0 +1,3 @@
+3000001 xxx
+3000004 xxx
+3000005 ..
diff --git a/test/stats.chk b/test/stats.chk
index e23ca31..6b2dd3b 100644
--- a/test/stats.chk
+++ b/test/stats.chk
@@ -1,6 +1,7 @@
 SN	0	number of samples:	3
 SN	1	number of samples:	3
 SN	0	number of records:	0
+SN	0	number of no-ALTs:	0
 SN	0	number of SNPs:	0
 SN	0	number of MNPs:	0
 SN	0	number of indels:	0
@@ -8,6 +9,7 @@ SN	0	number of others:	0
 SN	0	number of multiallelic sites:	0
 SN	0	number of multiallelic SNP sites:	0
 SN	1	number of records:	0
+SN	1	number of no-ALTs:	0
 SN	1	number of SNPs:	0
 SN	1	number of MNPs:	0
 SN	1	number of indels:	0
@@ -15,6 +17,7 @@ SN	1	number of others:	0
 SN	1	number of multiallelic sites:	0
 SN	1	number of multiallelic SNP sites:	0
 SN	2	number of records:	3
+SN	2	number of no-ALTs:	0
 SN	2	number of SNPs:	3
 SN	2	number of MNPs:	0
 SN	2	number of indels:	0
@@ -69,12 +72,12 @@ SN	2	number of samples:	3
 GCsAF	2	49.000000	2	1	0	1	2	3	0.375000	2
 NRDs	2	85.714286	33.333333	66.666667	100.000000
 NRDi	2	0.000000	0.000000	0.000000	0.000000
-GCsS	2	A	100.000	2	0	0	1	0	0
-GCsS	2	B	66.667	0	1	0	0	2	0
-GCsS	2	C	100.000	0	0	0	0	0	3
-GCiS	2	A	0.000	0	0	0	0	0	0
-GCiS	2	B	0.000	0	0	0	0	0	0
-GCiS	2	C	0.000	0	0	0	0	0	0
+GCsS	2	A	100.000	2	0	0	1	0	0	0
+GCsS	2	B	66.667	0	1	0	0	2	0	0
+GCsS	2	C	100.000	0	0	0	0	0	3	0
+GCiS	2	A	0.000	0	0	0	0	0	0	0
+GCiS	2	B	0.000	0	0	0	0	0	0	0
+GCiS	2	C	0.000	0	0	0	0	0	0	0
 PSC	0	A	0	0	0	0	0	0	0.0	0
 PSC	0	B	0	0	0	0	0	0	0.0	0
 PSC	0	C	0	0	0	0	0	0	0.0	0
@@ -84,4 +87,13 @@ PSC	1	C	0	0	0	0	0	0	0.0	0
 PSC	2	A	3	0	0	0	0	0	0.0	0
 PSC	2	B	0	0	3	3	0	0	0.0	0
 PSC	2	C	0	3	0	3	0	0	0.0	0
+PSI	0	A	0	0	0	0.00	0	0
+PSI	0	B	0	0	0	0.00	0	0
+PSI	0	C	0	0	0	0.00	0	0
+PSI	1	A	0	0	0	0.00	0	0
+PSI	1	B	0	0	0	0.00	0	0
+PSI	1	C	0	0	0	0.00	0	0
+PSI	2	A	0	0	0	0.00	0	0
+PSI	2	B	0	0	0	0.00	0	0
+PSI	2	C	0	0	0	0.00	0	0
 HWE	2	49.000000	3	0.330000	0.330000	0.330000
diff --git a/test/test-rbuf.c b/test/test-rbuf.c
index c428339..bc8ebe9 100644
--- a/test/test-rbuf.c
+++ b/test/test-rbuf.c
@@ -64,7 +64,7 @@ int main(int argc, char **argv)
     debug_print(&rbuf, dat);
 
     printf("Expanding:\n");
-    rbuf_expand0(&rbuf,int,dat);
+    rbuf_expand0(&rbuf,int,rbuf.n+1,dat);
     debug_print(&rbuf, dat);
 
     free(dat);
diff --git a/test/test.pl b/test/test.pl
index 24051ed..899ea16 100755
--- a/test/test.pl
+++ b/test/test.pl
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
 #
-#   Copyright (C) 2012-2014 Genome Research Ltd.
+#   Copyright (C) 2012-2015 Genome Research Ltd.
 #
 #   Author: Petr Danecek <pd3 at sanger.ac.uk>
 #
@@ -44,6 +44,7 @@ test_vcf_idxstats($opts,in=>'idx',args=>'-n',out=>'idx_count.out');
 test_vcf_idxstats($opts,in=>'empty',args=>'-s',out=>'empty.idx.out');
 test_vcf_idxstats($opts,in=>'empty',args=>'-n',out=>'empty.idx_count.out');
 test_vcf_check($opts,in=>'check',out=>'check.chk');
+test_vcf_check_merge($opts,in=>'check',out=>'check_merge.chk');
 test_vcf_stats($opts,in=>['stats.a','stats.b'],out=>'stats.chk',args=>'-s -');
 test_vcf_isec($opts,in=>['isec.a','isec.b'],out=>'isec.ab.out',args=>'-n =2');
 test_vcf_isec($opts,in=>['isec.a','isec.b'],out=>'isec.ab.flt.out',args=>'-n =2 -i"STRLEN(REF)==2"');
@@ -81,10 +82,27 @@ test_vcf_query($opts,in=>'query.filter',out=>'query.14.out',args=>q[-f'%POS[ %GT
 test_vcf_query($opts,in=>'query.filter',out=>'query.15.out',args=>q[-f'%POS[ %GT]\\n' -e'GT ="1"']);
 test_vcf_query($opts,in=>'query.filter',out=>'query.16.out',args=>q[-f'%POS[ %GT]\\n' -e'GT!="1"']);
 test_vcf_query($opts,in=>'query.2',out=>'query.17.out',args=>q[-f'%XX_A %XX.A %XX.A0 %xx.a0\\n']);
+test_vcf_query($opts,in=>'missing',out=>'query.18.out',args=>q[-i'IINT="."'  -f'%POS %IINT\\n']);
+test_vcf_query($opts,in=>'missing',out=>'query.19.out',args=>q[-i'IINT!="."' -f'%POS %IINT\\n']);
+test_vcf_query($opts,in=>'missing',out=>'query.18.out',args=>q[-e'IINT!="."' -f'%POS %IINT\\n']);
+test_vcf_query($opts,in=>'missing',out=>'query.19.out',args=>q[-e'IINT="."'  -f'%POS %IINT\\n']);
+test_vcf_query($opts,in=>'missing',out=>'query.20.out',args=>q[-i'IFLT="."'  -f'%POS %IFLT\\n']);
+test_vcf_query($opts,in=>'missing',out=>'query.21.out',args=>q[-i'IFLT!="."' -f'%POS %IFLT\\n']);
+test_vcf_query($opts,in=>'missing',out=>'query.20.out',args=>q[-e'IFLT!="."' -f'%POS %IFLT\\n']);
+test_vcf_query($opts,in=>'missing',out=>'query.21.out',args=>q[-e'IFLT="."'  -f'%POS %IFLT\\n']);
+test_vcf_query($opts,in=>'missing',out=>'query.22.out',args=>q[-i'ISTR="."'  -f'%POS %ISTR\\n']);
+test_vcf_query($opts,in=>'missing',out=>'query.23.out',args=>q[-i'ISTR!="."' -f'%POS %ISTR\\n']);
+test_vcf_query($opts,in=>'missing',out=>'query.23.out',args=>q[-e'ISTR="."'  -f'%POS %ISTR\\n']);
+test_vcf_query($opts,in=>'missing',out=>'query.22.out',args=>q[-e'ISTR!="."' -f'%POS %ISTR\\n']);
 test_vcf_norm($opts,in=>'norm',out=>'norm.out',fai=>'norm');
 test_vcf_norm($opts,in=>'norm.split',out=>'norm.split.out',args=>'-m-');
+test_vcf_norm($opts,in=>'norm.split.2',out=>'norm.split.2.out',args=>'-m-');
+test_vcf_norm($opts,in=>'norm.split',fai=>'norm',out=>'norm.split.and.norm.out',args=>'-m-');
 test_vcf_norm($opts,in=>'norm.merge',out=>'norm.merge.out',args=>'-m+');
+test_vcf_norm($opts,in=>'norm.merge.2',out=>'norm.merge.2.out',args=>'-m+');
+test_vcf_norm($opts,in=>'norm.merge.3',out=>'norm.merge.3.out',args=>'-m+');
 test_vcf_norm($opts,in=>'norm.merge',out=>'norm.merge.strict.out',args=>'-m+ -s');
+test_vcf_norm($opts,in=>'norm.setref',out=>'norm.setref.out',args=>'-Nc s',fai=>'norm');
 test_vcf_view($opts,in=>'view',out=>'view.1.out',args=>'-aUc1 -C1 -s NA00002 -v snps',reg=>'');
 test_vcf_view($opts,in=>'view',out=>'view.2.out',args=>'-f PASS -Xks NA00003',reg=>'-r20,Y');
 test_vcf_view($opts,in=>'view',out=>'view.3.out',args=>'-xs NA00003',reg=>'');
@@ -97,6 +115,9 @@ test_vcf_view($opts,in=>'view',out=>'view.9.out',args=>q[-GVsnps],reg=>'');
 test_vcf_view($opts,in=>'view',out=>'view.10.out',args=>q[-ne 'INDEL=1 || PV4[0]<0.006'],reg=>'');
 test_vcf_view($opts,in=>'view',out=>'view.exclude.out',args=>'-s ^NA00003',reg=>'');
 test_vcf_view($opts,in=>'view.omitgenotypes',out=>'view.omitgenotypes.out',args=>'',reg=>'');
+test_vcf_view($opts,in=>'view.omitgenotypes',out=>'view.dropgenotypes.out',args=>'-G',reg=>'');
+test_vcf_view($opts,in=>'view.omitgenotypes',out=>'view.dropgenotypes.noheader.out',args=>'-HG',reg=>'');
+test_vcf_view($opts,in=>'many.alleles',out=>'many.alleles.trim.out',args=>'-a',reg=>'');
 test_vcf_view($opts,in=>'view.vectors',out=>'view.vectors.A.out',args=>'-asA',reg=>'');
 test_vcf_view($opts,in=>'view.vectors',out=>'view.vectors.B.out',args=>'-asB',reg=>'');
 test_vcf_view($opts,in=>'view.filter',out=>'view.filter.1.out',args=>q[-H -i'FMT/FGS[0]="AAAAAA"'],reg=>'');    # test expressions
@@ -105,6 +126,7 @@ test_vcf_view($opts,in=>'view.filter',out=>'view.filter.3.out',args=>q[-H -i'FMT
 test_vcf_view($opts,in=>'view.filter',out=>'view.filter.4.out',args=>q[-H -i'FMT/FRS[1]="BB"'],reg=>'');
 test_vcf_view($opts,in=>'view.filter',out=>'view.filter.5.out',args=>q[-H -i'TXT0="text"'],reg=>'');
 test_vcf_view($opts,in=>'view.chrs',out=>'view.chrs.out',args=>'',reg=>'',tgts=>'view.chrs.tab');
+test_vcf_view($opts,in=>'filter.2',out=>'filter.11.out',args=>q[-i 'POS>=3062917'],reg=>'1:3062917-3157410');
 test_vcf_filter($opts,in=>'view.filter',out=>'view.filter.6.out',args=>q[-S. -e'TXT0="text"'],reg=>'');
 test_vcf_filter($opts,in=>'view.filter',out=>'view.filter.7.out',args=>q[-S. -e'FMT/FRS[1]="BB"'],reg=>'');
 test_vcf_filter($opts,in=>'view.filter',out=>'view.filter.8.out',args=>q[-S. -e'FMT/FGS[0]="AAAAAA"'],reg=>'');
@@ -114,9 +136,18 @@ test_vcf_filter($opts,in=>'view.filter',out=>'view.filter.11.out',args=>q[-S. -e
 test_vcf_view($opts,in=>'view.minmaxac',out=>'view.minmaxac.1.out',args=>q[-H -C5:nonmajor],reg=>'');
 test_vcf_view($opts,in=>'view.minmaxac',out=>'view.minmaxac.2.out',args=>q[-H -c6:nonmajor],reg=>'');
 test_vcf_view($opts,in=>'view.minmaxac',out=>'view.minmaxac.1.out',args=>q[-H -q0.3:major],reg=>'');
+test_vcf_view($opts,in=>'view.filter.annovar',out=>'view.filter.annovar.1.out',args=>q[-H -i 'Gene.refGene=="RAD21L1"'],reg=>'');
+test_vcf_view($opts,in=>'view.filter.annovar',out=>'view.filter.annovar.2.out',args=>q[-H -i 'Gene.refGene~"NOD"'],reg=>'');
+test_vcf_view($opts,in=>'view.filter.annovar',out=>'view.filter.annovar.3.out',args=>q[-H -i 'LJB2_MutationTaster=="0.291000"'],reg=>'');
 test_vcf_call($opts,in=>'mpileup',out=>'mpileup.1.out',args=>'-mv');
-test_vcf_call($opts,in=>'mpileup',out=>'mpileup.2.out',args=>'-mvg0');
+test_vcf_call($opts,in=>'mpileup',out=>'mpileup.2.out',args=>'-mg0');
+test_vcf_call($opts,in=>'mpileup.X',out=>'mpileup.X.out',args=>'-mv --ploidy-file {PATH}/mpileup.ploidy -S {PATH}/mpileup.samples');
+test_vcf_call($opts,in=>'mpileup.X',out=>'mpileup.X.out',args=>'-mv --ploidy-file {PATH}/mpileup.ploidy -S {PATH}/mpileup.ped');
 test_vcf_call_cAls($opts,in=>'mpileup',out=>'mpileup.cAls.out',tab=>'mpileup');
+test_vcf_call($opts,in=>'mpileup.c',out=>'mpileup.c.1.out',args=>'-cv');
+# test_vcf_call($opts,in=>'mpileup.c',out=>'mpileup.c.2.out',args=>'-cg0');
+test_vcf_call($opts,in=>'mpileup.c.X',out=>'mpileup.c.X.out',args=>'-cv --ploidy-file {PATH}/mpileup.ploidy -S {PATH}/mpileup.samples');
+test_vcf_call($opts,in=>'mpileup.c.X',out=>'mpileup.c.X.out',args=>'-cv --ploidy-file {PATH}/mpileup.ploidy -S {PATH}/mpileup.ped');
 test_vcf_filter($opts,in=>'filter.1',out=>'filter.1.out',args=>'-mx -g2 -G2');
 test_vcf_filter($opts,in=>'filter.2',out=>'filter.2.out',args=>q[-e'QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))' -sModified -S.]);
 test_vcf_filter($opts,in=>'filter.3',out=>'filter.3.out',args=>q[-e'DP=19'],fmt=>'%POS\\t%FILTER\\t%DP[\\t%GT]\\n');
@@ -131,6 +162,9 @@ test_vcf_filter($opts,in=>'filter.3',out=>'filter.6.out',args=>q[-e'FMT/GT="0/2"
 test_vcf_filter($opts,in=>'filter.3',out=>'filter.7.out',args=>q[-e'FMT/GT="0/2"' -s XX -m+x],fmt=>'%POS\\t%FILTER\\t%DP[\\t%GT]\\n');
 test_vcf_filter($opts,in=>'filter.2',out=>'filter.8.out',args=>q[-i'FMT/GT="0/0" && AC[*]=2'],fmt=>'%POS\\t%AC[\\t%GT]\\n');
 test_vcf_filter($opts,in=>'filter.2',out=>'filter.8.out',args=>q[-i'AC[*]=2 && FMT/GT="0/0"'],fmt=>'%POS\\t%AC[\\t%GT]\\n');
+test_vcf_filter($opts,in=>'filter.2',out=>'filter.9.out',args=>q[-i'ALT="."'],fmt=>'%POS\\t%AC[\\t%GT]\\n');
+test_vcf_filter($opts,in=>'filter.4',out=>'filter.10.out',args=>q[-S . -i 'FORMAT/TEST3<25']);
+test_vcf_filter($opts,in=>'filter.4',out=>'filter.10.out',args=>q[-S . -i 'FORMAT/TEST4<25']);
 test_vcf_regions($opts,in=>'regions');
 test_vcf_annotate($opts,in=>'annotate',tab=>'annotate',out=>'annotate.out',args=>'-c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL');
 test_vcf_annotate($opts,in=>'annotate',tab=>'annotate2',out=>'annotate2.out',args=>'-c CHROM,FROM,TO,T_STR');
@@ -142,11 +176,16 @@ test_vcf_annotate($opts,in=>'annotate3',out=>'annotate7.out',args=>'-x FORMAT');
 test_vcf_annotate($opts,in=>'annotate4',vcf=>'annots4',out=>'annotate8.out',args=>'-c +INFO');
 test_vcf_annotate($opts,in=>'annotate4',tab=>'annots4',out=>'annotate8.out',args=>'-c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR');
 test_vcf_plugin($opts,in=>'plugin1',out=>'missing2ref.out',cmd=>'+missing2ref');
+test_vcf_plugin($opts,in=>'plugin1',out=>'missing2ref.out',cmd=>'+setGT',args=>'-- -t . -n 0');
+test_vcf_annotate($opts,in=>'annotate9',tab=>'annots9',out=>'annotate9.out',args=>'-c CHROM,POS,REF,ALT,+ID');
 test_vcf_plugin($opts,in=>'plugin1',out=>'fill-AN-AC.out',cmd=>'+fill-AN-AC');
 test_vcf_plugin($opts,in=>'plugin1',out=>'dosage.out',cmd=>'+dosage');
 test_vcf_plugin($opts,in=>'fixploidy',out=>'fixploidy.out',cmd=>'+fixploidy',args=>'-- -s {PATH}/fixploidy.samples -p {PATH}/fixploidy.ploidy');
 test_vcf_plugin($opts,in=>'vcf2sex',out=>'vcf2sex.out',cmd=>'+vcf2sex',args=>'-- -n 5');
-test_vcf_plugin($opts,in=>'vcf2sex',out=>'vcf2sex.out',cmd=>'+vcf2sex',args=>'-- -gn 5');
+test_vcf_plugin($opts,in=>'vcf2sex',out=>'vcf2sex.out',cmd=>'+vcf2sex',args=>'-- -g GT');
+test_vcf_plugin($opts,in=>'vcf2sex',out=>'vcf2sex.out',cmd=>'+vcf2sex',args=>'-- -g GT -n 5');
+test_vcf_plugin($opts,in=>'view.GL',out=>'view.PL.vcf',cmd=>'+tag2tag',args=>'-- -r --gl-to-pl');
+test_vcf_plugin($opts,in=>'merge.a',out=>'fill-tags.out',cmd=>'+fill-tags');
 test_vcf_concat($opts,in=>['concat.1.a','concat.1.b'],out=>'concat.1.vcf.out',do_bcf=>0,args=>'');
 test_vcf_concat($opts,in=>['concat.1.a','concat.1.b'],out=>'concat.1.bcf.out',do_bcf=>1,args=>'');
 test_vcf_concat($opts,in=>['concat.2.a','concat.2.b'],out=>'concat.2.vcf.out',do_bcf=>0,args=>'-a');
@@ -172,9 +211,11 @@ test_vcf_convert($opts,in=>'check',out=>'check.gs.vcfids_chrom.samples',args=>'-
 test_vcf_convert($opts,in=>'convert',out=>'convert.hls.haps',args=>'-h -,.,.');
 test_vcf_convert($opts,in=>'convert',out=>'convert.hls.legend',args=>'-h .,-,.');
 test_vcf_convert($opts,in=>'convert',out=>'convert.hls.samples',args=>'-h .,.,-');
+test_vcf_convert_hls2vcf($opts,h=>'convert.hls.gt.hap',l=>'convert.hls.gt.legend',s=>'convert.hls.gt.samples',out=>'convert.gt.noHead.vcf',args=>'-H');
+test_vcf_convert_hs2vcf($opts,h=>'convert.hs.gt.hap',s=>'convert.hs.gt.samples',out=>'convert.gt.noHead.vcf',args=>'--hapsample2vcf');
 test_vcf_convert($opts,in=>'convert',out=>'convert.hs.hap',args=>'--hapsample -,.');
 test_vcf_convert($opts,in=>'convert',out=>'convert.hs.sample',args=>'--hapsample .,-');
-test_vcf_convert_gvcf($opts,in=>'convert.gvcf',out=>'convert.gvcf.out',args=>'--gvcf2vcf');
+test_vcf_convert_gvcf($opts,in=>'convert.gvcf',out=>'convert.gvcf.out',fa=>'gvcf.fa',args=>'--gvcf2vcf');
 test_vcf_convert_tsv2vcf($opts,in=>'convert.23andme',out=>'convert.23andme.vcf',args=>'-c ID,CHROM,POS,AA -s SAMPLE1',fai=>'23andme');
 test_vcf_consensus($opts,in=>'consensus',out=>'consensus.1.out',fa=>'consensus.fa',mask=>'consensus.tab',args=>'');
 test_vcf_consensus_chain($opts,in=>'consensus',out=>'consensus.1.chain',chain=>'consensus.1.chain',fa=>'consensus.fa',mask=>'consensus.tab',args=>'');
@@ -184,6 +225,9 @@ test_vcf_consensus($opts,in=>'consensus',out=>'consensus.3.out',fa=>'consensus.f
 test_vcf_consensus_chain($opts,in=>'consensus',out=>'consensus.3.chain',chain=>'consensus.3.chain',fa=>'consensus.fa',mask=>'consensus.tab',args=>'-i');
 test_vcf_consensus($opts,in=>'consensus',out=>'consensus.4.out',fa=>'consensus.fa',args=>'-H 1');
 test_vcf_consensus_chain($opts,in=>'consensus',out=>'consensus.4.chain',chain=>'consensus.4.chain',fa=>'consensus.fa',args=>'-H 1');
+test_vcf_consensus($opts,in=>'consensus2',out=>'consensus2.1.out',fa=>'consensus2.fa',args=>'-H 1');
+test_vcf_consensus($opts,in=>'consensus2',out=>'consensus2.2.out',fa=>'consensus2.fa',args=>'-H 2');
+test_vcf_consensus($opts,in=>'empty',out=>'consensus.5.out',fa=>'consensus.fa',args=>'');
 
 print "\nNumber of tests:\n";
 printf "    total   .. %d\n", $$opts{nok}+$$opts{nfailed};
@@ -402,6 +446,18 @@ sub test_vcf_check
     test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools stats -s - $$opts{tmp}/$args{in}.vcf.gz | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID\t'");
     test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools view -Ob $$opts{tmp}/$args{in}.vcf.gz | $$opts{bin}/bcftools stats -s - | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID\t'");
 }
+
+sub test_vcf_check_merge
+{
+    my ($opts,%args) = @_;
+    bgzip_tabix_vcf($opts,$args{in});
+    cmd("$$opts{bin}/bcftools stats -r 1 $$opts{tmp}/$args{in}.vcf.gz > $$opts{tmp}/$args{in}.1.chk");
+    cmd("$$opts{bin}/bcftools stats -r 2 $$opts{tmp}/$args{in}.vcf.gz > $$opts{tmp}/$args{in}.2.chk");
+    cmd("$$opts{bin}/bcftools stats -r 3 $$opts{tmp}/$args{in}.vcf.gz > $$opts{tmp}/$args{in}.3.chk");
+    cmd("$$opts{bin}/bcftools stats -r 4 $$opts{tmp}/$args{in}.vcf.gz > $$opts{tmp}/$args{in}.4.chk");
+    test_cmd($opts,%args,cmd=>"$$opts{bin}/plot-vcfstats -m $$opts{tmp}/$args{in}.1.chk $$opts{tmp}/$args{in}.2.chk $$opts{tmp}/$args{in}.3.chk $$opts{tmp}/$args{in}.4.chk | grep -v 'plot-vcfstats' | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID\t'");
+}
+
 sub test_vcf_stats
 {
     my ($opts,%args) = @_;
@@ -468,12 +524,26 @@ sub test_vcf_convert
     test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools convert $args{args} $$opts{tmp}/$args{in}.vcf.gz");
     test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools view -Ob $$opts{tmp}/$args{in}.vcf.gz | $$opts{bin}/bcftools convert $args{args}");
 }
+sub test_vcf_convert_hls2vcf
+{
+    my ($opts,%args) = @_;
+    my $hls = join(',', map { "$$opts{path}/$_" }( $args{h}, $args{l}, $args{s} ) );
+    test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools convert $args{args} $hls | grep -v ^##");
+    test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools convert $args{args} $hls -Ou | $$opts{bin}/bcftools view | grep -v ^##");
+}
+sub test_vcf_convert_hs2vcf
+{
+    my ($opts,%args) = @_;
+    my $hs = join(',', map { "$$opts{path}/$_" }( $args{h}, $args{s} ) );
+    test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools convert $args{args} $hs | grep -v ^##");
+    test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools convert $args{args} $hs -Ou | $$opts{bin}/bcftools view | grep -v ^##");
+}
 sub test_vcf_convert_gvcf
 {
     my ($opts,%args) = @_;
     bgzip_tabix_vcf($opts,$args{in});
-    test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools convert $args{args} $$opts{tmp}/$args{in}.vcf.gz | grep -v ^##bcftools");
-    test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools view -Ob $$opts{tmp}/$args{in}.vcf.gz | $$opts{bin}/bcftools convert $args{args} | grep -v ^##bcftools");
+    test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools convert $args{args} -f $$opts{path}/$args{fa} $$opts{tmp}/$args{in}.vcf.gz | grep -v ^##bcftools");
+    test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools view -Ob $$opts{tmp}/$args{in}.vcf.gz | $$opts{bin}/bcftools convert $args{args} -f $$opts{path}/$args{fa} | grep -v ^##bcftools");
 }
 sub test_vcf_convert_tsv2vcf
 {
@@ -509,6 +579,7 @@ sub test_vcf_view
 sub test_vcf_call
 {
     my ($opts,%args) = @_;
+    $args{args} =~ s/{PATH}/$$opts{path}/g;
     test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools call $args{args} $$opts{path}/$args{in}.vcf | grep -v ^##bcftools_");
     test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools call -Ob $args{args} $$opts{path}/$args{in}.vcf | $$opts{bin}/bcftools view | grep -v ^##bcftools_");
 }
@@ -666,7 +737,7 @@ sub test_vcf_annotate
         bgzip_tabix($opts,file=>$args{tab},suffix=>'tab',args=>'-s1 -b2 -e2');
         $annot_fname = "-a $$opts{tmp}/$args{tab}.tab.gz";
         $in_fname = "$$opts{path}/$args{in}.vcf";
-        $hdr = "-h $$opts{path}/$args{in}.hdr";
+        $hdr = -e "$$opts{path}/$args{in}.hdr" ? "-h $$opts{path}/$args{in}.hdr" : '';
     }
     elsif ( exists($args{vcf}) )
     {
diff --git a/test/view.9.out b/test/view.9.out
index b5b13bd..3529210 100644
--- a/test/view.9.out
+++ b/test/view.9.out
@@ -20,10 +20,6 @@
 ##INFO=<ID=QD,Number=1,Type=Float,Description="Variant confidence/quality by depth">
 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes">
 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
-##FORMAT=<ID=DP,Number=1,Type=Integer,Description="# high-quality bases">
-##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">
 ##FILTER=<ID=StrandBias,Description="Min P-value for strand bias (INFO/PV4) [0.0001]">
 ##FILTER=<ID=BaseQualBias,Description="Min P-value for baseQ bias (INFO/PV4) [1e-100]">
 ##FILTER=<ID=MapQualBias,Description="Min P-value for mapQ bias (INFO/PV4) [0]">
diff --git a/test/view.GL.vcf b/test/view.GL.vcf
new file mode 100644
index 0000000..6b8de70
--- /dev/null
+++ b/test/view.GL.vcf
@@ -0,0 +1,29 @@
+##fileformat=VCFv4.1
+##FILTER=<ID=PASS,Description="All filters passed">
+##reference=file:///seq/references/1000Genomes-NCBI37.fasta
+##contig=<ID=11,length=135006516>
+##contig=<ID=20,length=63025520>
+##contig=<ID=X,length=155270560>
+##contig=<ID=Y,length=59373566>
+##FORMAT=<ID=GL,Number=G,Type=Float,Description="List of Phred-scaled genotype likelihoods">
+##FILTER=<ID=StrandBias,Description="Min P-value for strand bias (INFO/PV4) [0.0001]">
+##FILTER=<ID=BaseQualBias,Description="Min P-value for baseQ bias (INFO/PV4) [1e-100]">
+##FILTER=<ID=MapQualBias,Description="Min P-value for mapQ bias (INFO/PV4) [0]">
+##FILTER=<ID=EndDistBias,Description="Min P-value for end distance bias (INFO/PV4) [0.0001]">
+##FILTER=<ID=MinAB,Description="Minimum number of alternate bases (INFO/DP4) [2]">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA00001	NA00002	NA00003
+11	2343543	.	A	.	999	PASS	.	GL	0,-25.5,-25.5	0,-25.5,-25.5	0,-25.5,-25.5
+11	5464562	.	C	T	999	PASS	.	GL	0,0,0	0,0,0	0,0,0
+20	76962	rs6111385	T	C	999	PASS	.	GL	-25.5,0,-25.5	-25.5,-25.5,0	-25.5,-25.5,0
+20	126310	.	ACC	A	999	StrandBias;EndDistBias	.	GL	-25.5,0,-13.2	-25.5,0,-13.9	-25.5,-21.3,0
+20	138125	rs2298108	G	T	999	PASS	.	GL	-13.5,0,-16.3	-14,0,-25.5	-25.5,-19.9,0
+20	138148	rs2298109	C	T	999	PASS	.	GL	-19.5,0,-25.5	-19.2,0,-25.5	-25.5,-23.5,0
+20	271225	.	T	TTTA,TA	999	StrandBias	.	GL	-15.1,-5.3,-20.3,0,-5.2,-15.9	-25.5,0,-21.3,-25.5,-25.5,-25.5	-25.5,-25.5,-25.5,-25.5,0,-24.1
+20	304568	.	C	T	999	PASS	.	GL	-9.5,0,-25.5	-19.2,0,-25.5	-25.5,-9.5,0
+20	326891	.	A	AC	999	PASS	.	GL	-25.5,0,-13.2	-25.5,0,-13.9	.,.,.
+X	2928329	rs62584840	C	T	999	PASS	.	GL	0,-5.6	0,-8.1	-7.3,0,-1.9
+X	2933066	rs61746890	G	C	999	PASS	.	GL	0,-25.5	0,-25.5	-25.5,-25.5,-25.5
+X	2942109	rs5939407	T	C	999	PASS	.	GL	0,-25.5	-25.5,0	-25.5,-15.7,0
+X	3048719	.	T	C	999	PASS	.	GL	0,-25.5	-25.5,0	-25.5,0,-15.7
+Y	8657215	.	C	A	999	PASS	.	GL	0,-25.5	-25.5,0	.
+Y	10011673	rs78249411	G	A	999	MinAB	.	GL	-12.6,-10.1	-9.5,0	.
diff --git a/test/view.PL.vcf b/test/view.PL.vcf
new file mode 100644
index 0000000..7d430ad
--- /dev/null
+++ b/test/view.PL.vcf
@@ -0,0 +1,29 @@
+##fileformat=VCFv4.1
+##FILTER=<ID=PASS,Description="All filters passed">
+##reference=file:///seq/references/1000Genomes-NCBI37.fasta
+##contig=<ID=11,length=135006516>
+##contig=<ID=20,length=63025520>
+##contig=<ID=X,length=155270560>
+##contig=<ID=Y,length=59373566>
+##FILTER=<ID=StrandBias,Description="Min P-value for strand bias (INFO/PV4) [0.0001]">
+##FILTER=<ID=BaseQualBias,Description="Min P-value for baseQ bias (INFO/PV4) [1e-100]">
+##FILTER=<ID=MapQualBias,Description="Min P-value for mapQ bias (INFO/PV4) [0]">
+##FILTER=<ID=EndDistBias,Description="Min P-value for end distance bias (INFO/PV4) [0.0001]">
+##FILTER=<ID=MinAB,Description="Minimum number of alternate bases (INFO/DP4) [2]">
+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Phred scaled genotype likelihoods">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA00001	NA00002	NA00003
+11	2343543	.	A	.	999	PASS	.	PL	0,255,255	0,255,255	0,255,255
+11	5464562	.	C	T	999	PASS	.	PL	0,0,0	0,0,0	0,0,0
+20	76962	rs6111385	T	C	999	PASS	.	PL	255,0,255	255,255,0	255,255,0
+20	126310	.	ACC	A	999	StrandBias;EndDistBias	.	PL	255,0,132	255,0,139	255,213,0
+20	138125	rs2298108	G	T	999	PASS	.	PL	135,0,163	140,0,255	255,199,0
+20	138148	rs2298109	C	T	999	PASS	.	PL	195,0,255	192,0,255	255,235,0
+20	271225	.	T	TTTA,TA	999	StrandBias	.	PL	151,53,203,0,52,159	255,0,213,255,255,255	255,255,255,255,0,241
+20	304568	.	C	T	999	PASS	.	PL	95,0,255	192,0,255	255,95,0
+20	326891	.	A	AC	999	PASS	.	PL	255,0,132	255,0,139	.,.,.
+X	2928329	rs62584840	C	T	999	PASS	.	PL	0,56	0,81	73,0,19
+X	2933066	rs61746890	G	C	999	PASS	.	PL	0,255	0,255	255,255,255
+X	2942109	rs5939407	T	C	999	PASS	.	PL	0,255	255,0	255,157,0
+X	3048719	.	T	C	999	PASS	.	PL	0,255	255,0	255,0,157
+Y	8657215	.	C	A	999	PASS	.	PL	0,255	255,0	.
+Y	10011673	rs78249411	G	A	999	MinAB	.	PL	126,101	95,0	.
diff --git a/test/view.dropgenotypes.noheader.out b/test/view.dropgenotypes.noheader.out
new file mode 100644
index 0000000..7b5a3c8
--- /dev/null
+++ b/test/view.dropgenotypes.noheader.out
@@ -0,0 +1,5 @@
+20	14370	rs6054257	G	A	29	PASS	NS=3;DP=14
+20	17330	.	T	A	3	PASS	NS=3;DP=11
+20	1110696	rs6040355	A	G,T	67	PASS	NS=2;DP=10
+20	1230237	.	T	.	47	PASS	NS=3;DP=13
+20	1234567	microsat1	GTC	G,GTCT	50	PASS	NS=3;DP=9
diff --git a/test/view.dropgenotypes.out b/test/view.dropgenotypes.out
new file mode 100644
index 0000000..8e983f6
--- /dev/null
+++ b/test/view.dropgenotypes.out
@@ -0,0 +1,12 @@
+##fileformat=VCFv4.2
+##FILTER=<ID=PASS,Description="All filters passed">
+##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta
+##contig=<ID=20,length=62435964,assembly=B36,md5=f126cdf8a6e0c7f379d618ff66beb2da,species="Homo sapiens",taxonomy=x>
+##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
+20	14370	rs6054257	G	A	29	PASS	NS=3;DP=14
+20	17330	.	T	A	3	PASS	NS=3;DP=11
+20	1110696	rs6040355	A	G,T	67	PASS	NS=2;DP=10
+20	1230237	.	T	.	47	PASS	NS=3;DP=13
+20	1234567	microsat1	GTC	G,GTCT	50	PASS	NS=3;DP=9
diff --git a/test/view.filter.annovar.1.out b/test/view.filter.annovar.1.out
new file mode 100644
index 0000000..e71068c
--- /dev/null
+++ b/test/view.filter.annovar.1.out
@@ -0,0 +1,2 @@
+20	1230237	.	T	G	47	PASS	NS=3;DP=13;AA=T;ANNOVAR_DATE=2015-06-17;Func.refGene=intronic;Gene.refGene=RAD21L1;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.ensGene=intronic;Gene.ensGene=ENSG00000244588;GeneDetail.ensGene=.;ExonicFunc.ensGene=.;AAChange.ensGene=.;esp6500si_ea=.;esp6500si_all=.;1000g2012apr_eur=.;1000g2012apr_all=.;snp138=.;LJB2_SIFT=.;LJB2_PolyPhen2_HDIV=.;LJB2_PP2_HDIV_Pred=.;LJB2_PolyPhen2_HVAR=.;LJB2_PolyPhen2_HVAR_Pred=.;LJB2_LRT=.;LJB2_LRT_Pred=.;LJ [...]
+20	1230288	.	T	.	50	PASS	NS=3;DP=13;AA=T;ANNOVAR_DATE=2015-06-17;Func.refGene=intronic;Gene.refGene=RAD21L1;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.ensGene=intronic;Gene.ensGene=ENSG00000244588;GeneDetail.ensGene=.;ExonicFunc.ensGene=.;AAChange.ensGene=.;esp6500si_ea=.;esp6500si_all=.;1000g2012apr_eur=.;1000g2012apr_all=.;snp138=.;LJB2_SIFT=.;LJB2_PolyPhen2_HDIV=.;LJB2_PP2_HDIV_Pred=.;LJB2_PolyPhen2_HVAR=.;LJB2_PolyPhen2_HVAR_Pred=.;LJB2_LRT=.;LJB2_LRT_Pred=.;LJ [...]
diff --git a/test/view.filter.annovar.2.out b/test/view.filter.annovar.2.out
new file mode 100644
index 0000000..6ac94a1
--- /dev/null
+++ b/test/view.filter.annovar.2.out
@@ -0,0 +1 @@
+16	50745926	rs2066844	C	T	80	PASS	NS=3;DP=14;AF=0.5;DB;H2;ANNOVAR_DATE=2015-06-17;Func.refGene=exonic;Gene.refGene=NOD2;GeneDetail.refGene=.;ExonicFunc.refGene=nonsynonymous_SNV;AAChange.refGene=NOD2:NM_001293557:exon3:c.C2023T:p.R675W,NOD2:NM_022162:exon4:c.C2104T:p.R702W;Func.ensGene=exonic;Gene.ensGene=ENSG00000167207;GeneDetail.ensGene=.;ExonicFunc.ensGene=nonsynonymous_SNV;AAChange.ensGene=ENSG00000167207:ENST00000300589:exon4:c.C2104T:p.R702W;esp6500si_ea=0.043488;esp6500si_all=0.0 [...]
diff --git a/test/view.filter.annovar.3.out b/test/view.filter.annovar.3.out
new file mode 100644
index 0000000..6ac94a1
--- /dev/null
+++ b/test/view.filter.annovar.3.out
@@ -0,0 +1 @@
+16	50745926	rs2066844	C	T	80	PASS	NS=3;DP=14;AF=0.5;DB;H2;ANNOVAR_DATE=2015-06-17;Func.refGene=exonic;Gene.refGene=NOD2;GeneDetail.refGene=.;ExonicFunc.refGene=nonsynonymous_SNV;AAChange.refGene=NOD2:NM_001293557:exon3:c.C2023T:p.R675W,NOD2:NM_022162:exon4:c.C2104T:p.R702W;Func.ensGene=exonic;Gene.ensGene=ENSG00000167207;GeneDetail.ensGene=.;ExonicFunc.ensGene=nonsynonymous_SNV;AAChange.ensGene=ENSG00000167207:ENST00000300589:exon4:c.C2104T:p.R702W;esp6500si_ea=0.043488;esp6500si_all=0.0 [...]
diff --git a/test/view.filter.annovar.vcf b/test/view.filter.annovar.vcf
new file mode 100644
index 0000000..7613667
--- /dev/null
+++ b/test/view.filter.annovar.vcf
@@ -0,0 +1,52 @@
+##fileformat=VCFv4.0
+##fileDate=20090805
+##source=myImputationProgramV3.1
+##reference=1000GenomesPilot-NCBI36
+##phasing=partial
+##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
+##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency">
+##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele">
+##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership, build 129">
+##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2 membership">
+##FILTER=<ID=q10,Description="Quality below 10">
+##FILTER=<ID=s50,Description="Less than 50% of samples have data">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
+##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">
+##INFO=<ID=ANNOVAR_DATE,Number=1,Type=String,Description="Flag the start of ANNOVAR annotation for one alternative allele">
+##INFO=<ID=Gene.refGene,Number=.,Type=String,Description="Gene.refGene annotation provided by ANNOVAR">
+##INFO=<ID=GeneDetail.refGene,Number=.,Type=String,Description="GeneDetail.refGene annotation provided by ANNOVAR">
+##INFO=<ID=ExonicFunc.refGene,Number=.,Type=String,Description="ExonicFunc.refGene annotation provided by ANNOVAR">
+##INFO=<ID=AAChange.refGene,Number=.,Type=String,Description="AAChange.refGene annotation provided by ANNOVAR">
+##INFO=<ID=Func.ensGene,Number=.,Type=String,Description="Func.ensGene annotation provided by ANNOVAR">
+##INFO=<ID=Gene.ensGene,Number=.,Type=String,Description="Gene.ensGene annotation provided by ANNOVAR">
+##INFO=<ID=GeneDetail.ensGene,Number=.,Type=String,Description="GeneDetail.ensGene annotation provided by ANNOVAR">
+##INFO=<ID=ExonicFunc.ensGene,Number=.,Type=String,Description="ExonicFunc.ensGene annotation provided by ANNOVAR">
+##INFO=<ID=AAChange.ensGene,Number=.,Type=String,Description="AAChange.ensGene annotation provided by ANNOVAR">
+##INFO=<ID=esp6500si_ea,Number=1,Type=Float,Description="esp6500si_ea annotation provided by ANNOVAR">
+##INFO=<ID=esp6500si_all,Number=1,Type=Float,Description="esp6500si_all annotation provided by ANNOVAR">
+##INFO=<ID=1000g2012apr_eur,Number=1,Type=Float,Description="1000g2012apr_eur annotation provided by ANNOVAR">
+##INFO=<ID=1000g2012apr_all,Number=1,Type=Float,Description="1000g2012apr_all annotation provided by ANNOVAR">
+##INFO=<ID=snp138,Number=.,Type=String,Description="snp138 annotation provided by ANNOVAR">
+##INFO=<ID=LJB2_SIFT,Number=.,Type=String,Description="LJB2_SIFT annotation provided by ANNOVAR">
+##INFO=<ID=LJB2_PolyPhen2_HDIV,Number=.,Type=String,Description="LJB2_PolyPhen2_HDIV annotation provided by ANNOVAR">
+##INFO=<ID=LJB2_PP2_HDIV_Pred,Number=.,Type=String,Description="LJB2_PP2_HDIV_Pred annotation provided by ANNOVAR">
+##INFO=<ID=LJB2_PolyPhen2_HVAR,Number=.,Type=String,Description="LJB2_PolyPhen2_HVAR annotation provided by ANNOVAR">
+##INFO=<ID=LJB2_PolyPhen2_HVAR_Pred,Number=.,Type=String,Description="LJB2_PolyPhen2_HVAR_Pred annotation provided by ANNOVAR">
+##INFO=<ID=LJB2_LRT,Number=.,Type=String,Description="LJB2_LRT annotation provided by ANNOVAR">
+##INFO=<ID=LJB2_LRT_Pred,Number=.,Type=String,Description="LJB2_LRT_Pred annotation provided by ANNOVAR">
+##INFO=<ID=LJB2_MutationTaster,Number=1,Type=String,Description="LJB2_MutationTaster annotation provided by ANNOVAR">
+##INFO=<ID=LJB2_MutationTaster_Pred,Number=.,Type=String,Description="LJB2_MutationTaster_Pred annotation provided by ANNOVAR">
+##INFO=<ID=LJB_MutationAssessor,Number=.,Type=String,Description="LJB_MutationAssessor annotation provided by ANNOVAR">
+##INFO=<ID=LJB_MutationAssessor_Pred,Number=1,Type=String,Description="LJB_MutationAssessor_Pred annotation provided by ANNOVAR">
+##INFO=<ID=LJB2_FATHMM,Number=.,Type=String,Description="LJB2_FATHMM annotation provided by ANNOVAR">
+##INFO=<ID=LJB2_GERP++,Number=.,Type=String,Description="LJB2_GERP++ annotation provided by ANNOVAR">
+##INFO=<ID=LJB2_PhyloP,Number=.,Type=String,Description="LJB2_PhyloP annotation provided by ANNOVAR">
+##INFO=<ID=LJB2_SiPhy,Number=.,Type=String,Description="LJB2_SiPhy annotation provided by ANNOVAR">
+##INFO=<ID=ALLELE_END,Number=0,Type=Flag,Description="Flag the end of ANNOVAR annotation for one alternative allele">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA00001	NA00002	NA00003
+16	50745926	rs2066844	C	T	80	PASS	NS=3;DP=14;AF=0.5;DB;H2;ANNOVAR_DATE=2015-06-17;Func.refGene=exonic;Gene.refGene=NOD2;GeneDetail.refGene=.;ExonicFunc.refGene=nonsynonymous_SNV;AAChange.refGene=NOD2:NM_001293557:exon3:c.C2023T:p.R675W,NOD2:NM_022162:exon4:c.C2104T:p.R702W;Func.ensGene=exonic;Gene.ensGene=ENSG00000167207;GeneDetail.ensGene=.;ExonicFunc.ensGene=nonsynonymous_SNV;AAChange.ensGene=ENSG00000167207:ENST00000300589:exon4:c.C2104T:p.R702W;esp6500si_ea=0.043488;esp6500si_all=0.0 [...]
+20	1230237	.	T	G	47	PASS	NS=3;DP=13;AA=T;ANNOVAR_DATE=2015-06-17;Func.refGene=intronic;Gene.refGene=RAD21L1;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.ensGene=intronic;Gene.ensGene=ENSG00000244588;GeneDetail.ensGene=.;ExonicFunc.ensGene=.;AAChange.ensGene=.;esp6500si_ea=.;esp6500si_all=.;1000g2012apr_eur=.;1000g2012apr_all=.;snp138=.;LJB2_SIFT=.;LJB2_PolyPhen2_HDIV=.;LJB2_PP2_HDIV_Pred=.;LJB2_PolyPhen2_HVAR=.;LJB2_PolyPhen2_HVAR_Pred=.;LJB2_LRT=.;LJB2_LRT_Pred=.;LJ [...]
+20	1230288	.	T	.	50	PASS	NS=3;DP=13;AA=T;ANNOVAR_DATE=2015-06-17;Func.refGene=intronic;Gene.refGene=RAD21L1;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.ensGene=intronic;Gene.ensGene=ENSG00000244588;GeneDetail.ensGene=.;ExonicFunc.ensGene=.;AAChange.ensGene=.;esp6500si_ea=.;esp6500si_all=.;1000g2012apr_eur=.;1000g2012apr_all=.;snp138=.;LJB2_SIFT=.;LJB2_PolyPhen2_HDIV=.;LJB2_PP2_HDIV_Pred=.;LJB2_PolyPhen2_HVAR=.;LJB2_PolyPhen2_HVAR_Pred=.;LJB2_LRT=.;LJB2_LRT_Pred=.;LJ [...]
diff --git a/vcfannotate.c b/vcfannotate.c
index 00630a5..96a1649 100644
--- a/vcfannotate.c
+++ b/vcfannotate.c
@@ -66,6 +66,7 @@ annot_line_t;
 #define REPLACE_MISSING  0  // replace only missing values
 #define REPLACE_ALL      1  // replace both missing and existing values
 #define REPLACE_EXISTING 2  // replace only if tgt is not missing
+#define SET_OR_APPEND    3  // set new value if missing or non-existent, append otherwise
 typedef struct _annot_col_t
 {
     int icol, replace, number;  // number: one of BCF_VL_* types
@@ -78,12 +79,15 @@ annot_col_t;
 #define FLT_INCLUDE 1
 #define FLT_EXCLUDE 2
 
+#define MARK_LISTED   1
+#define MARK_UNLISTED 2
+
 typedef struct _args_t
 {
     bcf_srs_t *files;
     bcf_hdr_t *hdr, *hdr_out;
     htsFile *out_fh;
-    int output_type;
+    int output_type, n_threads;
     bcf_sr_regions_t *tgts;
 
     filter_t *filter;
@@ -115,8 +119,8 @@ typedef struct _args_t
     kstring_t tmpks;
 
     char **argv, *output_fname, *targets_fname, *regions_list, *header_fname;
-    char *remove_annots, *columns, *rename_chrs, *sample_names;
-    int argc, drop_header, tgts_is_vcf;
+    char *remove_annots, *columns, *rename_chrs, *sample_names, *mark_sites;
+    int argc, drop_header, tgts_is_vcf, mark_sites_logic;
 }
 args_t;
 
@@ -306,7 +310,7 @@ static void init_remove_annots(args_t *args)
         ss = *se ? se+1 : se;
     }
     free(str.s);
-    if ( keep_flt || keep_info || keep_flt )
+    if ( keep_flt || keep_info || keep_fmt )
     {
         int j;
         for (j=0; j<args->hdr->nhrec; j++)
@@ -359,41 +363,52 @@ static void init_header_lines(args_t *args)
 }
 static int setter_filter(args_t *args, bcf1_t *line, annot_col_t *col, void *data)
 {
+    // note: so far this works only with one filter, not a list of filters
     annot_line_t *tab = (annot_line_t*) data;
+    if ( tab->cols[col->icol] && tab->cols[col->icol][0]=='.' && !tab->cols[col->icol][1] ) return 0; // don't replace with "."
     hts_expand(int,1,args->mtmpi,args->tmpi);
     args->tmpi[0] = bcf_hdr_id2int(args->hdr_out, BCF_DT_ID, tab->cols[col->icol]);
     if ( args->tmpi[0]<0 ) error("The FILTER is not defined in the header: %s\n", tab->cols[col->icol]);
+    if ( col->replace==SET_OR_APPEND ) { bcf_add_filter(args->hdr_out,line,args->tmpi[0]); return 0; }
     if ( col->replace!=REPLACE_MISSING )
+    {
+        bcf_update_filter(args->hdr_out,line,NULL,0);
+        bcf_update_filter(args->hdr_out,line,args->tmpi,1); 
+        return 0; 
+    }
+    
+    // only update missing FILTER
+    if ( !(line->unpacked & BCF_UN_FLT) ) bcf_unpack(line, BCF_UN_FLT);
+    if ( !line->d.n_flt )
         bcf_update_filter(args->hdr_out,line,args->tmpi,1);
-    else
-        bcf_add_filter(args->hdr_out,line,args->tmpi[0]);
     return 0;
 }
 static int vcf_setter_filter(args_t *args, bcf1_t *line, annot_col_t *col, void *data)
 {
+    int i;
     bcf1_t *rec = (bcf1_t*) data;
     if ( !(rec->unpacked & BCF_UN_FLT) ) bcf_unpack(rec, BCF_UN_FLT);
-    hts_expand(int,rec->d.n_flt,args->mtmpi,args->tmpi);
-    int i;
-    if ( col->replace!=REPLACE_MISSING )
+    if ( !(line->unpacked & BCF_UN_FLT) ) bcf_unpack(line, BCF_UN_FLT);
+    if ( !rec->d.n_flt ) return 0;  // don't overwrite with a missing value
+    if ( col->replace==SET_OR_APPEND || col->replace==REPLACE_MISSING )
     {
+        if ( col->replace==REPLACE_MISSING && line->d.n_flt ) return 0; // only update missing FILTER
         for (i=0; i<rec->d.n_flt; i++)
         {
             const char *flt = bcf_hdr_int2id(args->files->readers[1].header, BCF_DT_ID, rec->d.flt[i]);
-            args->tmpi[i] = bcf_hdr_id2int(args->hdr_out, BCF_DT_ID, flt);
+            bcf_add_filter(args->hdr_out,line,bcf_hdr_id2int(args->hdr_out, BCF_DT_ID, flt));
         }
-        bcf_update_filter(args->hdr_out,line,args->tmpi,rec->d.n_flt);
         return 0;
     }
-    else
+    hts_expand(int,rec->d.n_flt,args->mtmpi,args->tmpi);
+    for (i=0; i<rec->d.n_flt; i++)
     {
-        for (i=0; i<rec->d.n_flt; i++)
-        {
-            const char *flt = bcf_hdr_int2id(args->files->readers[1].header, BCF_DT_ID, rec->d.flt[i]);
-            bcf_add_filter(args->hdr_out,line,bcf_hdr_id2int(args->hdr_out, BCF_DT_ID, flt));
-        }
-        return 0;
+        const char *flt = bcf_hdr_int2id(args->files->readers[1].header, BCF_DT_ID, rec->d.flt[i]);
+        args->tmpi[i] = bcf_hdr_id2int(args->hdr_out, BCF_DT_ID, flt);
     }
+    bcf_update_filter(args->hdr_out,line,NULL,0);
+    bcf_update_filter(args->hdr_out,line,args->tmpi,rec->d.n_flt);
+    return 0;
 }
 static int setter_id(args_t *args, bcf1_t *line, annot_col_t *col, void *data)
 {
@@ -401,13 +416,14 @@ static int setter_id(args_t *args, bcf1_t *line, annot_col_t *col, void *data)
     //      IN  ANNOT   OUT     ACHIEVED_BY
     //      x   y       x        -c +ID
     //      x   y       y        -c ID
-    //      x   y       x,y      /not supported/
+    //      x   y       x,y      -c =ID
     //      x   .       x        -c +ID, ID
     //      x   .       .        -x ID
     //      .   y       y        -c +ID, -c ID
     //
     annot_line_t *tab = (annot_line_t*) data;
     if ( tab->cols[col->icol] && tab->cols[col->icol][0]=='.' && !tab->cols[col->icol][1] ) return 0; // don't replace with "."
+    if ( col->replace==SET_OR_APPEND ) return bcf_add_id(args->hdr_out,line,tab->cols[col->icol]);
     if ( col->replace!=REPLACE_MISSING ) return bcf_update_id(args->hdr_out,line,tab->cols[col->icol]);
 
     // running with +ID, only update missing ids
@@ -419,6 +435,7 @@ static int vcf_setter_id(args_t *args, bcf1_t *line, annot_col_t *col, void *dat
 {
     bcf1_t *rec = (bcf1_t*) data;
     if ( rec->d.id && rec->d.id[0]=='.' && !rec->d.id[1] ) return 0;    // don't replace with "."
+    if ( col->replace==SET_OR_APPEND ) return bcf_add_id(args->hdr_out,line,rec->d.id);
     if ( col->replace!=REPLACE_MISSING ) return bcf_update_id(args->hdr_out,line,rec->d.id);
 
     // running with +ID, only update missing ids
@@ -1117,6 +1134,7 @@ static void init_columns(args_t *args)
         int replace = REPLACE_ALL;
         if ( *ss=='+' ) { replace = REPLACE_MISSING; ss++; }
         else if ( *ss=='-' ) { replace = REPLACE_EXISTING; ss++; }
+        else if ( *ss=='=' ) { replace = SET_OR_APPEND; ss++; }
         i++;
         str.l = 0;
         kputsn(ss, se-ss, &str);
@@ -1129,7 +1147,7 @@ static void init_columns(args_t *args)
         else if ( !strcasecmp("ALT",str.s) ) args->alt_idx = i;
         else if ( !strcasecmp("ID",str.s) )
         {
-            if ( replace==REPLACE_EXISTING ) error("todo: -ID\n");
+            if ( replace==REPLACE_EXISTING ) error("Apologies, the -ID feature has not been implemented yet.\n");
             args->ncols++; args->cols = (annot_col_t*) realloc(args->cols,sizeof(annot_col_t)*args->ncols);
             annot_col_t *col = &args->cols[args->ncols-1];
             col->icol = i;
@@ -1139,7 +1157,7 @@ static void init_columns(args_t *args)
         }
         else if ( !strcasecmp("FILTER",str.s) )
         {
-            if ( replace==REPLACE_EXISTING ) error("todo: -FILTER\n");
+            if ( replace==REPLACE_EXISTING ) error("Apologies, the -FILTER feature has not been implemented yet.\n");
             args->ncols++; args->cols = (annot_col_t*) realloc(args->cols,sizeof(annot_col_t)*args->ncols);
             annot_col_t *col = &args->cols[args->ncols-1];
             col->icol = i;
@@ -1165,7 +1183,8 @@ static void init_columns(args_t *args)
         }
         else if ( !strcasecmp("QUAL",str.s) )
         {
-            if ( replace==REPLACE_EXISTING ) error("todo: -QUAL\n");
+            if ( replace==REPLACE_EXISTING ) error("Apologies, the -QUAL feature has not been implemented yet.\n");
+            if ( replace==SET_OR_APPEND ) error("Apologies, the =QUAL feature has not been implemented yet.\n");
             args->ncols++; args->cols = (annot_col_t*) realloc(args->cols,sizeof(annot_col_t)*args->ncols);
             annot_col_t *col = &args->cols[args->ncols-1];
             col->icol = i;
@@ -1175,7 +1194,8 @@ static void init_columns(args_t *args)
         }
         else if ( args->tgts_is_vcf && !strcasecmp("INFO",str.s) ) // All INFO fields
         {
-            if ( replace==REPLACE_EXISTING ) error("todo: -INFO/TAG\n");
+            if ( replace==REPLACE_EXISTING ) error("Apologies, the -INFO/TAG feature has not been implemented yet.\n");
+            if ( replace==SET_OR_APPEND ) error("Apologies, the =INFO/TAG feature has not been implemented yet.\n");
             bcf_hdr_t *tgts_hdr = args->files->readers[1].header;
             int j;
             for (j=0; j<tgts_hdr->nhrec; j++)
@@ -1240,8 +1260,11 @@ static void init_columns(args_t *args)
                     }
             }
         }
-        else if ( args->tgts_is_vcf && (!strncasecmp("FORMAT/",str.s, 7) || !strncasecmp("FMT/",str.s,4)) )
+        else if ( !strncasecmp("FORMAT/",str.s, 7) || !strncasecmp("FMT/",str.s,4) )
         {
+            if ( !args->tgts_is_vcf )
+                error("Error: FORMAT fields can be carried over from a VCF file only.\n");
+
             char *key = str.s + (!strncasecmp("FMT/",str.s,4) ? 4 : 7);
             if ( force_samples<0 ) force_samples = replace;
             if ( force_samples>=0 && replace!=REPLACE_ALL ) force_samples = replace;;
@@ -1268,7 +1291,8 @@ static void init_columns(args_t *args)
         }
         else
         {
-            if ( replace==REPLACE_EXISTING ) error("todo: -INFO/TAG\n");
+            if ( replace==REPLACE_EXISTING ) error("Apologies, the -INFO/TAG feature has not been implemented yet.\n");
+            if ( replace==SET_OR_APPEND ) error("Apologies, the =INFO/TAG feature has not been implemented yet.\n");
             if ( !strncasecmp("INFO/",str.s,5) ) { memmove(str.s,str.s+5,str.l-4); }
             int hdr_id = bcf_hdr_id2int(args->hdr_out, BCF_DT_ID, str.s);
             if ( !bcf_hdr_idinfo_exists(args->hdr_out,BCF_HL_INFO,hdr_id) )
@@ -1387,6 +1411,14 @@ static void init_data(args_t *args)
         args->set_ids = convert_init(args->hdr_out, NULL, 0, args->set_ids_fmt);
     }
 
+    if ( args->mark_sites )
+    {
+        if ( !args->targets_fname ) error("The -a option not given\n");
+        if ( args->tgts_is_vcf ) error("Apologies, this has not been implemented yet: -a is a VCF\n");  // very easy to add..
+        bcf_hdr_printf(args->hdr_out,"##INFO=<ID=%s,Number=0,Type=Flag,Description=\"Sites %slisted in %s\">",
+            args->mark_sites,args->mark_sites_logic==MARK_LISTED?"":"not ",args->mark_sites);
+    }
+
     bcf_hdr_append_version(args->hdr_out, args->argc, args->argv, "bcftools_annotate");
     if ( !args->drop_header )
     {
@@ -1394,6 +1426,7 @@ static void init_data(args_t *args)
 
         args->out_fh = hts_open(args->output_fname,hts_bcf_wmode(args->output_type));
         if ( args->out_fh == NULL ) error("Can't write to \"%s\": %s\n", args->output_fname, strerror(errno));
+        if ( args->n_threads ) hts_set_threads(args->out_fh, args->n_threads);
         bcf_hdr_write(args->out_fh, args->hdr_out);
     }
 }
@@ -1542,9 +1575,20 @@ static void annotate(args_t *args, bcf1_t *line)
 
         if ( i<args->nalines )
         {
+            // there is a matching line
             for (j=0; j<args->ncols; j++)
                 if ( args->cols[j].setter(args,line,&args->cols[j],&args->alines[i]) )
                     error("fixme: Could not set %s at %s:%d\n", args->cols[j].hdr_key,bcf_seqname(args->hdr,line),line->pos+1);
+
+        }
+
+        if ( args->mark_sites )
+        {
+            // ideally, we'd like to be far more general than this in future, see https://github.com/samtools/bcftools/issues/87
+            if ( args->mark_sites_logic==MARK_LISTED )
+                bcf_update_info_flag(args->hdr_out,line,args->mark_sites,NULL,i<args->nalines?1:0);
+            else
+                bcf_update_info_flag(args->hdr_out,line,args->mark_sites,NULL,i<args->nalines?0:1);
         }
     }
     else if ( args->files->nreaders == 2 && bcf_sr_has_line(args->files,1) )
@@ -1582,6 +1626,7 @@ static void usage(args_t *args)
     fprintf(stderr, "   -h, --header-lines <file>      lines which should be appended to the VCF header\n");
     fprintf(stderr, "   -I, --set-id [+]<format>       set ID column, see man pagee for details\n");
     fprintf(stderr, "   -i, --include <expr>           select sites for which the expression is true (see man pagee for details)\n");
+    fprintf(stderr, "   -m, --mark-sites [+-]<tag>     add INFO/tag flag to sites which are (\"+\") or are not (\"-\") listed in the -a file\n");
     fprintf(stderr, "   -o, --output <file>            write output to a file [standard output]\n");
     fprintf(stderr, "   -O, --output-type <b|u|z|v>    b: compressed BCF, u: uncompressed BCF, z: compressed VCF, v: uncompressed VCF [v]\n");
     fprintf(stderr, "   -r, --regions <region>         restrict to comma-separated list of regions\n");
@@ -1590,6 +1635,7 @@ static void usage(args_t *args)
     fprintf(stderr, "   -s, --samples [^]<list>        comma separated list of samples to annotate (or exclude with \"^\" prefix)\n");
     fprintf(stderr, "   -S, --samples-file [^]<file>   file of samples to annotate (or exclude with \"^\" prefix)\n");
     fprintf(stderr, "   -x, --remove <list>            list of annotations to remove (e.g. ID,INFO/DP,FORMAT/DP,FILTER). See man page for details\n");
+    fprintf(stderr, "       --threads <int>            number of extra output compression threads [0]\n");
     fprintf(stderr, "\n");
     exit(1);
 }
@@ -1602,31 +1648,40 @@ int main_vcfannotate(int argc, char *argv[])
     args->files   = bcf_sr_init();
     args->output_fname = "-";
     args->output_type = FT_VCF;
+    args->n_threads = 0;
     args->ref_idx = args->alt_idx = args->chr_idx = args->from_idx = args->to_idx = -1;
     args->set_ids_replace = 1;
     int regions_is_file = 0;
 
     static struct option loptions[] =
     {
-        {"set-id",1,0,'I'},
-        {"output",1,0,'o'},
-        {"output-type",1,0,'O'},
-        {"annotations",1,0,'a'},
-        {"include",1,0,'i'},
-        {"exclude",1,0,'e'},
-        {"regions",1,0,'r'},
-        {"regions-file",1,0,'R'},
-        {"remove",1,0,'x'},
-        {"columns",1,0,'c'},
-        {"rename-chrs",1,0,1},
-        {"header-lines",1,0,'h'},
-        {"samples",1,0,'s'},
-        {"samples-file",1,0,'S'},
-        {0,0,0,0}
+        {"mark-sites",required_argument,NULL,'m'},
+        {"set-id",required_argument,NULL,'I'},
+        {"output",required_argument,NULL,'o'},
+        {"output-type",required_argument,NULL,'O'},
+        {"threads",required_argument,NULL,9},
+        {"annotations",required_argument,NULL,'a'},
+        {"include",required_argument,NULL,'i'},
+        {"exclude",required_argument,NULL,'e'},
+        {"regions",required_argument,NULL,'r'},
+        {"regions-file",required_argument,NULL,'R'},
+        {"remove",required_argument,NULL,'x'},
+        {"columns",required_argument,NULL,'c'},
+        {"rename-chrs",required_argument,NULL,1},
+        {"header-lines",required_argument,NULL,'h'},
+        {"samples",required_argument,NULL,'s'},
+        {"samples-file",required_argument,NULL,'S'},
+        {NULL,0,NULL,0}
     };
-    while ((c = getopt_long(argc, argv, "h:?o:O:r:R:a:x:c:i:e:S:s:I:",loptions,NULL)) >= 0)
+    while ((c = getopt_long(argc, argv, "h:?o:O:r:R:a:x:c:i:e:S:s:I:m:",loptions,NULL)) >= 0)
     {
         switch (c) {
+            case 'm': 
+                args->mark_sites_logic = MARK_LISTED;
+                if ( optarg[0]=='+' ) args->mark_sites = optarg+1;
+                else if ( optarg[0]=='-' ) { args->mark_sites = optarg+1; args->mark_sites_logic = MARK_UNLISTED; }
+                else args->mark_sites = optarg; 
+                break;
             case 'I': args->set_ids_fmt = optarg; break;
             case 's': args->sample_names = optarg; break;
             case 'S': args->sample_names = optarg; args->sample_is_file = 1; break;
@@ -1649,6 +1704,7 @@ int main_vcfannotate(int argc, char *argv[])
             case 'R': args->regions_list = optarg; regions_is_file = 1; break;
             case 'h': args->header_fname = optarg; break;
             case  1 : args->rename_chrs = optarg; break;
+            case  9 : args->n_threads = strtol(optarg, 0, 0); break;
             case '?': usage(args); break;
             default: error("Unknown argument: %s\n", optarg);
         }
diff --git a/vcfcall.c b/vcfcall.c
index dab7cb7..a28caee 100644
--- a/vcfcall.c
+++ b/vcfcall.c
@@ -34,10 +34,13 @@ THE SOFTWARE.  */
 #include <stdarg.h>
 #include <htslib/kfunc.h>
 #include <htslib/synced_bcf_reader.h>
+#include <htslib/khash_str2int.h>
 #include <ctype.h>
 #include "bcftools.h"
 #include "call.h"
 #include "prob1.h"
+#include "ploidy.h"
+#include "gvcf.h"
 
 void error(const char *format, ...);
 
@@ -49,7 +52,7 @@ void error(const char *format, ...);
 #define CF_NO_GENO      1
 #define CF_INS_MISSED   (1<<1)
 #define CF_CCALL        (1<<2)
-#define CF_GVCF         (1<<3)
+//                      (1<<3)
 //                      (1<<4)
 //                      (1<<5)
 #define CF_ACGT_ONLY    (1<<6)
@@ -65,17 +68,23 @@ void error(const char *format, ...);
 typedef struct
 {
     int flag;   // combination of CF_* flags above
-    int output_type;
+    int output_type, n_threads;
     htsFile *bcf_in, *out_fh;
     char *bcf_fname, *output_fname;
     char **samples;             // for subsampling and ploidy
-    int nsamples, *samples_map;
+    int nsamples, *samples_map; // mapping from output sample names to original VCF
     char *regions, *targets;    // regions to process
     int regions_is_file, targets_is_file;
 
+    char *samples_fname;
+    int samples_is_file;
+    int *sample2sex;    // mapping for ploidy. If negative, interpreted as -1*ploidy
+    int *sex2ploidy, *sex2ploidy_prev, nsex;
+    ploidy_t *ploidy;
+    gvcf_t *gvcf;
+
     bcf1_t *missed_line;
     call_t aux;     // parameters and temporary data
-    gvcf_t gvcf;
 
     int argc;
     char **argv;
@@ -92,43 +101,96 @@ typedef struct
 }
 args_t;
 
-static family_t *get_family(family_t *fam, int nfam, char *name)
+static char **add_sample(void *name2idx, char **lines, int *nlines, int *mlines, char *name, char sex, int *ith)
 {
-    int i;
-    for (i=0; i<nfam; i++)
-    {
-        if ( !strcmp(fam[i].name, name) ) return &fam[i];
-    }
-    return NULL;
+    int ret = khash_str2int_get(name2idx, name, ith);
+    if ( ret==0 ) return lines;
+
+    hts_expand(char*,(*nlines+1),*mlines,lines);
+    int len = strlen(name);
+    lines[*nlines] = (char*) malloc(len+3);
+    memcpy(lines[*nlines],name,len);
+    lines[*nlines][len]   = ' ';
+    lines[*nlines][len+1] = sex;
+    lines[*nlines][len+2] = 0;
+    *ith = *nlines;
+    (*nlines)++;
+    khash_str2int_set(name2idx, strdup(name), *ith);
+    return lines;
+}
+
+typedef struct
+{
+    const char *alias, *about, *ploidy;
 }
+ploidy_predef_t;
 
-static char **add_sample(char **sam, int *n, int *m, char *name, int ploidy, int *ith)
+static ploidy_predef_t ploidy_predefs[] =
 {
-    int i;
-    for (i=0; i<*n; i++)
+    { .alias  = "GRCh37",
+      .about  = "Human Genome reference assembly GRCh37 / hg19",
+      .ploidy =
+          "X 1 60000 M 1\n"
+          "X 2699521 154931043 M 1\n"
+          "Y 1 59373566 M 1\n"
+          "Y 1 59373566 F 0\n"
+          "MT 1 16569 M 1\n"
+          "MT 1 16569 F 1\n"
+          "chrX 1 60000 M 1\n"
+          "chrX 2699521 154931043 M 1\n"
+          "chrY 1 59373566 M 1\n"
+          "chrY 1 59373566 F 0\n"
+          "chrM 1 16569 M 1\n"
+          "chrM 1 16569 F 1\n"
+          "*  * *     M 2\n"
+          "*  * *     F 2\n"
+    },
+    { .alias  = "GRCh38",
+      .about  = "Human Genome reference assembly GRCh38 / hg38, plain chromosome naming (1,2,3,..)",
+      .ploidy =
+          "X 1 9999 M 1\n"
+          "X 2781480 155701381 M 1\n"
+          "Y 1 57227415 M 1\n"
+          "Y 1 57227415 F 0\n"
+          "MT 1 16569 M 1\n"
+          "MT 1 16569 F 1\n"
+          "chrX 1 9999 M 1\n"
+          "chrX 2781480 155701381 M 1\n"
+          "chrY 1 57227415 M 1\n"
+          "chrY 1 57227415 F 0\n"
+          "chrM 1 16569 M 1\n"
+          "chrM 1 16569 F 1\n"
+          "*  * *     M 2\n"
+          "*  * *     F 2\n"
+    },
+    { .alias  = "X",
+      .about  = "Treat male samples as haploid and female as diploid regardless of the chromosome name",
+      .ploidy =
+          "*  * *     M 1\n"
+          "*  * *     F 2\n"
+    },
+    { .alias  = "Y",
+      .about  = "Treat male samples as haploid and female as no-copy, regardless of the chromosome name",
+      .ploidy =
+          "*  * *     M 1\n"
+          "*  * *     F 0\n"
+    },
     {
-        if ( !strcmp(sam[i], name) )
-        {
-            *ith = i;
-            return sam;
-        }
+        .alias  = NULL,
+        .about  = NULL,
+        .ploidy = NULL,
     }
-    hts_expand(char*,(*n+1),*m,sam);
-    int len = strlen(name);
-    sam[*n] = (char*) malloc(len+2);
-    memcpy(sam[*n],name,len+1);
-    sam[*n][len+1] = ploidy;
-    *ith = *n;
-    (*n)++;
-    return sam;
-}
+};
 
-static char **parse_ped_samples(call_t *call, char **vals, int _n)
+// only 5 columns are required and the first is ignored:
+//  ignored,sample,father(or 0),mother(or 0),sex(1=M,2=F)
+static char **parse_ped_samples(call_t *call, char **vals, int nvals, int *nsmpl)
 {
-    int i, j, max = 0, n = 0;
-    kstring_t str = {0,0,0};
-    char **sam = NULL;
-    for (i=0; i<_n; i++)
+    int i, j, mlines = 0, nlines = 0;
+    kstring_t str = {0,0,0}, fam_str = {0,0,0};
+    void *name2idx = khash_str2int_init();
+    char **lines = NULL;
+    for (i=0; i<nvals; i++)
     {
         str.l = 0;
         kputs(vals[i], &str);
@@ -149,49 +211,38 @@ static char **parse_ped_samples(call_t *call, char **vals, int _n)
         }
         if ( j!=5 ) break;
 
-        family_t *fam = get_family(call->fams, call->nfams, str.s);
-        if ( !fam )
+        char sex = col_ends[3][1]=='1' ? 'M' : 'F';
+        lines = add_sample(name2idx, lines, &nlines, &mlines, col_ends[0]+1, sex, &j);
+        if ( strcmp(col_ends[1]+1,"0") && strcmp(col_ends[2]+1,"0") )   // father and mother
         {
             call->nfams++;
             hts_expand(family_t, call->nfams, call->mfams, call->fams);
-            fam = &call->fams[call->nfams-1];
-            fam->name = strdup(str.s);
-            for (j=0; j<3; j++) fam->sample[j] = -1;
-        }
-
-        int ploidy = 2;
-        if ( call->flag & (CALL_CHR_X|CALL_CHR_Y) )
-        {
-            if ( col_ends[3][1]=='1' ) ploidy = 1; // male: one chrX and one chrY copy
-            else
-                ploidy = call->flag & CALL_CHR_X ? 2 : 0; // female: two chrX copies, no chrY
-        }
-        sam = add_sample(sam, &n, &max, col_ends[0]+1, ploidy, &j);
-        if ( strcmp(col_ends[1]+1,"0") )    // father
-        {
-            if ( fam->sample[CHILD]>=0 ) error("Multiple childs in %s [%s,%s]\n", str.s, sam[j],sam[fam->sample[CHILD]]);
-            fam->sample[CHILD] = j;
-            if ( fam->sample[FATHER]>=0 ) error("Two fathers in %s?\n", str.s);
-            sam = add_sample(sam, &n, &max, col_ends[1]+1, call->flag & (CALL_CHR_X|CALL_CHR_Y) ? 1 : 2, &fam->sample[FATHER]);
-        }
-        if ( strcmp(col_ends[2]+1,"0") )    // mother
-        {
-            if ( fam->sample[MOTHER]>=0 ) error("Two mothers in %s?\n", str.s);
-            sam = add_sample(sam, &n, &max, col_ends[2]+1, call->flag & CALL_CHR_Y ? 0 : 2, &fam->sample[MOTHER]);
+            family_t *fam = &call->fams[call->nfams-1];
+            fam_str.l = 0;
+            ksprintf(&fam_str,"father=%s, mother=%s, child=%s", col_ends[1]+1,col_ends[2]+1,col_ends[0]+1);
+            fam->name = strdup(fam_str.s);
+
+            if ( !khash_str2int_has_key(name2idx, col_ends[1]+1) )
+                lines = add_sample(name2idx, lines, &nlines, &mlines, col_ends[1]+1, 'M', &fam->sample[FATHER]);
+            if ( !khash_str2int_has_key(name2idx, col_ends[2]+1) )
+                lines = add_sample(name2idx, lines, &nlines, &mlines, col_ends[2]+1, 'F', &fam->sample[MOTHER]);
+
+            khash_str2int_get(name2idx, col_ends[0]+1, &fam->sample[CHILD]);
+            khash_str2int_get(name2idx, col_ends[1]+1, &fam->sample[FATHER]);
+            khash_str2int_get(name2idx, col_ends[2]+1, &fam->sample[MOTHER]);
         }
     }
     free(str.s);
+    free(fam_str.s);
+    khash_str2int_destroy_free(name2idx);
 
-    if ( i!=_n ) // not a ped file
+    if ( i!=nvals ) // not a ped file
     {
-        if ( i>0 ) error("Could not parse the samples, thought it was PED format, some rows have 5 columns?!\n");
+        if ( i>0 ) error("Could not parse samples, not a PED format.\n");
         return NULL;
     }
-    assert( n==_n );
-    for (i=0; i<call->nfams; i++)
-        assert( call->fams[i].sample[0]>=0 && call->fams[i].sample[1]>=0 && call->fams[i].sample[2]>=0 ); // multiple childs, not a trio
-
-    return sam;
+    *nsmpl = nlines;
+    return lines;
 }
 
 
@@ -200,44 +251,80 @@ static char **parse_ped_samples(call_t *call, char **vals, int _n)
  *  Alternatively, if no such file exists, the file name is interpreted
  *  as a comma-separated list of samples. When ploidy is not present,
  *  the default ploidy 2 is assumed.
- *
- *  Returns an array of sample names, where the byte value just after \0
- *  indicates the ploidy.
  */
-static char **read_samples(call_t *call, const char *fn, int is_file, int *_n)
+static void set_samples(args_t *args, const char *fn, int is_file)
 {
-    int i, n;
-    char **vals = hts_readlist(fn, is_file, &n);
-    if ( !vals ) error("Could not read the file: %s\n", fn);
+    int i, nlines;
+    char **lines = hts_readlist(fn, is_file, &nlines);
+    if ( !lines ) error("Could not read the file: %s\n", fn);
+
+    int nsmpls;
+    char **smpls = parse_ped_samples(&args->aux, lines, nlines, &nsmpls);
+    if ( smpls )
+    {
+        for (i=0; i<nlines; i++) free(lines[i]);
+        free(lines);
+        lines = smpls;
+        nlines = nsmpls;
+    }
+
+    args->samples_map = (int*) malloc(sizeof(int)*bcf_hdr_nsamples(args->aux.hdr)); // for subsetting
+    args->sample2sex  = (int*) malloc(sizeof(int)*bcf_hdr_nsamples(args->aux.hdr));
+    int dflt_sex_id = ploidy_add_sex(args->ploidy, "F");
+    for (i=0; i<bcf_hdr_nsamples(args->aux.hdr); i++) args->sample2sex[i] = dflt_sex_id;
 
-    char **smpls = parse_ped_samples(call, vals, n);
-    if ( !smpls )
+    int *old2new = (int*) malloc(sizeof(int)*bcf_hdr_nsamples(args->aux.hdr));
+    for (i=0; i<bcf_hdr_nsamples(args->aux.hdr); i++) old2new[i] = -1;
+
+    int nsmpl = 0, map_needed = 0;
+    for (i=0; i<nlines; i++)
     {
-        smpls = (char**) malloc(sizeof(char*)*n);
-        for (i=0; i<n; i++)
+        char *ss = lines[i];
+        while ( *ss && isspace(*ss) ) ss++;
+        if ( !*ss ) error("Could not parse: %s\n", lines[i]);
+        if ( *ss=='#' ) continue;
+        char *se = ss;
+        while ( *se && !isspace(*se) ) se++;
+        char x = *se, *xptr = se; *se = 0;
+
+        int ismpl = bcf_hdr_id2int(args->aux.hdr, BCF_DT_SAMPLE, ss);
+        if ( ismpl < 0 ) { fprintf(stderr,"Warning: No such sample in the VCF: %s\n",ss); continue; }
+
+        ss = se+1;
+        while ( *ss && isspace(*ss) ) ss++;
+        if ( !*ss ) ss = "2";   // default ploidy
+        se = ss;
+        while ( *se && !isspace(*se) ) se++;
+        if ( se==ss ) { *xptr = x; error("Could not parse: \"%s\"\n", lines[i]); }
+
+        if ( ss[1]==0 && (ss[0]=='0' || ss[0]=='1' || ss[0]=='2') )
+            args->sample2sex[nsmpl] = -1*(ss[0]-'0');
+        else
+            args->sample2sex[nsmpl] = ploidy_add_sex(args->ploidy, ss);
+
+        if ( ismpl!=nsmpl ) map_needed = 1;
+        args->samples_map[nsmpl] = ismpl;
+        old2new[ismpl] = nsmpl;
+        nsmpl++;
+    }
+
+    for (i=0; i<args->aux.nfams; i++)
+    {
+        int j, nmiss = 0;
+        family_t *fam = &args->aux.fams[i];
+        for (j=0; j<3; j++)
         {
-            char *s = vals[i];
-            while ( *s && !isspace(*s) ) s++;
-            int len = s-vals[i];
-            smpls[i] = (char*) malloc(len+2);
-            strncpy(smpls[i],vals[i],len);
-            smpls[i][len] = 0;
-            while ( *s && isspace(*s) ) s++;
-            int x = 2;
-            if ( *s )
-            {
-                x = (int)s[0] - '0'; // Convert ASCII digit to decimal
-                if (x != 0 && x != 1 && x != 2) error("Ploidy can only be 0, 1 or 2: %s\n", vals[i]);
-            }
-            smpls[i][len+1] = x;
+            fam->sample[i] = old2new[fam->sample[i]];
+            if ( fam->sample[i]<0 ) nmiss++;
         }
+        assert( nmiss==0 || nmiss==3 );
     }
+    free(old2new);
 
-    for (i=0; i<n; i++) free(vals[i]);
-    free(vals);
+    if ( !map_needed ) { free(args->samples_map); args->samples_map = NULL; }
 
-    *_n = n;
-    return smpls;
+    args->nsamples = nsmpl;
+    args->samples = lines;
 }
 
 static void init_missed_line(args_t *args)
@@ -259,8 +346,6 @@ static void print_missed_line(bcf_sr_regions_t *regs, void *data)
     call_t *call = &args->aux;
     bcf1_t *missed = args->missed_line;
 
-    if ( args->flag & CF_GVCF ) error("todo: Combine --gvcf and --insert-missed\n");
-
     char *ss = regs->line.s;
     int i = 0;
     while ( i<args->aux.srs->targets_als-1 && *ss )
@@ -299,13 +384,32 @@ static void init_data(args_t *args)
             error("Failed to read the targets: %s\n", args->regions);
     }
 
-    int i;
     if ( !bcf_sr_add_reader(args->aux.srs, args->bcf_fname) ) error("Failed to open %s: %s\n", args->bcf_fname,bcf_sr_strerror(args->aux.srs->errnum));
+    args->aux.hdr = bcf_sr_get_header(args->aux.srs,0);
 
-    if ( args->nsamples && args->nsamples != bcf_hdr_nsamples(args->aux.srs->readers[0].header) )
+    int i;
+    if ( args->samples_fname )
     {
-        args->samples_map = (int *) malloc(sizeof(int)*args->nsamples);
-        args->aux.hdr = bcf_hdr_subset(args->aux.srs->readers[0].header, args->nsamples, args->samples, args->samples_map);
+        set_samples(args, args->samples_fname, args->samples_is_file);
+        if ( args->aux.flag&CALL_CONSTR_TRIO )
+        {
+            if ( 3*args->aux.nfams!=args->nsamples ) error("Expected only trios in %s, sorry!\n", args->samples_fname);
+            fprintf(stderr,"Detected %d samples in %d trio families\n", args->nsamples,args->aux.nfams);
+        }
+        args->nsex = ploidy_nsex(args->ploidy);
+        args->sex2ploidy = (int*) calloc(args->nsex,sizeof(int));
+        args->sex2ploidy_prev = (int*) calloc(args->nsex,sizeof(int));
+        args->aux.ploidy = (uint8_t*) malloc(args->nsamples);
+        for (i=0; i<args->nsamples; i++) args->aux.ploidy[i] = 2;
+        for (i=0; i<args->nsex; i++) args->sex2ploidy_prev[i] = 2;
+    }
+
+    if ( args->gvcf ) 
+        gvcf_update_header(args->gvcf, args->aux.hdr);
+
+    if ( args->samples_map )
+    {
+        args->aux.hdr = bcf_hdr_subset(bcf_sr_get_header(args->aux.srs,0), args->nsamples, args->samples, args->samples_map);
         if ( !args->aux.hdr ) error("Error occurred while subsetting samples\n");
         for (i=0; i<args->nsamples; i++)
             if ( args->samples_map[i]<0 ) error("No such sample: %s\n", args->samples[i]);
@@ -313,45 +417,15 @@ static void init_data(args_t *args)
     }
     else
     {
-        args->aux.hdr = bcf_hdr_dup(args->aux.srs->readers[0].header);
+        args->aux.hdr = bcf_hdr_dup(bcf_sr_get_header(args->aux.srs,0));
         for (i=0; i<args->nsamples; i++)
             if ( bcf_hdr_id2int(args->aux.hdr,BCF_DT_SAMPLE,args->samples[i])<0 )
                 error("No such sample: %s\n", args->samples[i]);
     }
 
-    // Reorder ploidy and family indexes to match mpileup's output and exclude samples which are not available
-    if ( args->aux.ploidy )
-    {
-        for (i=0; i<args->aux.nfams; i++)
-        {
-            int j;
-            for (j=0; j<3; j++)
-            {
-                int k = bcf_hdr_id2int(args->aux.hdr, BCF_DT_SAMPLE, args->samples[ args->aux.fams[i].sample[j] ]);
-                if ( k<0 ) error("No such sample: %s\n", args->samples[ args->aux.fams[i].sample[j] ]);
-                args->aux.fams[i].sample[j] = k;
-            }
-        }
-        uint8_t *ploidy = (uint8_t*) calloc(bcf_hdr_nsamples(args->aux.hdr), 1);
-        for (i=0; i<args->nsamples; i++)    // i index in -s sample list
-        {
-            int j = bcf_hdr_id2int(args->aux.hdr, BCF_DT_SAMPLE, args->samples[i]);     // j index in the output VCF / subset VCF
-            if ( j<0 )
-            {
-                fprintf(stderr,"Warning: no such sample: \"%s\"\n", args->samples[i]);
-                continue;
-            }
-            ploidy[j] = args->aux.ploidy[i];
-        }
-        args->nsamples = bcf_hdr_nsamples(args->aux.hdr);
-        for (i=0; i<args->nsamples; i++)
-            assert( ploidy[i]==0 || ploidy[i]==1 || ploidy[i]==2 );
-        free(args->aux.ploidy);
-        args->aux.ploidy = ploidy;
-    }
-
     args->out_fh = hts_open(args->output_fname, hts_bcf_wmode(args->output_type));
     if ( args->out_fh == NULL ) error("Can't write to \"%s\": %s\n", args->output_fname, strerror(errno));
+    if ( args->n_threads ) hts_set_threads(args->out_fh, args->n_threads);
 
     if ( args->flag & CF_QCALL )
         return;
@@ -362,19 +436,6 @@ static void init_data(args_t *args)
     if ( args->flag & CF_CCALL )
         ccall_init(&args->aux);
 
-    if ( args->flag&CF_GVCF )
-    {
-        bcf_hdr_append(args->aux.hdr,"##INFO=<ID=END,Number=1,Type=Integer,Description=\"End position of the variant described in this record\">");
-        args->gvcf.rid  = -1;
-        args->gvcf.line = bcf_init1();
-        args->gvcf.gt   = (int32_t*) malloc(2*sizeof(int32_t)*bcf_hdr_nsamples(args->aux.hdr));
-        for (i=0; i<bcf_hdr_nsamples(args->aux.hdr); i++)
-        {
-            args->gvcf.gt[2*i+0] = bcf_gt_unphased(0);
-            args->gvcf.gt[2*i+1] = bcf_gt_unphased(0);
-        }
-    }
-
     bcf_hdr_remove(args->aux.hdr, BCF_HL_INFO, "QS");
     bcf_hdr_remove(args->aux.hdr, BCF_HL_INFO, "I16");
 
@@ -397,12 +458,14 @@ static void destroy_data(args_t *args)
         free(args->aux.fams);
     }
     if ( args->missed_line ) bcf_destroy(args->missed_line);
-    if ( args->gvcf.line ) bcf_destroy(args->gvcf.line);
-    free(args->gvcf.gt);
-    free(args->gvcf.dp);
+    ploidy_destroy(args->ploidy);
+    free(args->sex2ploidy);
+    free(args->sex2ploidy_prev);
     free(args->samples);
     free(args->samples_map);
+    free(args->sample2sex);
     free(args->aux.ploidy);
+    if ( args->gvcf ) gvcf_destroy(args->gvcf);
     bcf_hdr_destroy(args->aux.hdr);
     hts_close(args->out_fh);
     bcf_sr_destroy(args->aux.srs);
@@ -451,6 +514,59 @@ static int parse_format_flag(const char *str)
     return flag;
 }
 
+static void set_ploidy(args_t *args, bcf1_t *rec)
+{
+    ploidy_query(args->ploidy,(char*)bcf_seqname(args->aux.hdr,rec),rec->pos,args->sex2ploidy,NULL,NULL);
+
+    int i;
+    for (i=0; i<args->nsex; i++)
+        if ( args->sex2ploidy[i]!=args->sex2ploidy_prev[i] ) break;
+
+    if ( i==args->nsex ) return;    // ploidy same as previously
+
+    for (i=0; i<args->nsamples; i++)
+    {
+        if ( args->sample2sex[i]<0 )
+            args->aux.ploidy[i] = -1*args->sample2sex[i];
+        else
+            args->aux.ploidy[i] = args->sex2ploidy[args->sample2sex[i]];
+    }
+
+    int *tmp = args->sex2ploidy; args->sex2ploidy = args->sex2ploidy_prev; args->sex2ploidy_prev = tmp;
+}
+
+ploidy_t *init_ploidy(char *alias)
+{
+    const ploidy_predef_t *pld = ploidy_predefs;
+
+    int detailed = 0, len = strlen(alias);
+    if ( alias[len-1]=='?' ) { detailed = 1; alias[len-1] = 0; }
+
+    while ( pld->alias && strcasecmp(alias,pld->alias) ) pld++;
+
+    if ( !pld->alias )
+    {
+        fprintf(stderr,"Predefined ploidies:\n");
+        pld = ploidy_predefs;
+        while ( pld->alias )
+        {
+            fprintf(stderr,"%s\n   .. %s\n\n", pld->alias,pld->about);
+            if ( detailed )
+                fprintf(stderr,"%s\n", pld->ploidy);
+            pld++;
+        }
+        fprintf(stderr,"Run as --ploidy <alias> (e.g. --ploidy GRCh37).\n");
+        fprintf(stderr,"To see the detailed ploidy definition, append a question mark (e.g. --ploidy GRCh37?).\n");
+        fprintf(stderr,"\n");
+        exit(-1);
+    }
+    else if ( detailed )
+    {
+        fprintf(stderr,"%s", pld->ploidy);
+        exit(-1);
+    }
+    return ploidy_init_string(pld->ploidy,2);
+}
 
 static void usage(args_t *args)
 {
@@ -465,17 +581,20 @@ static void usage(args_t *args)
     fprintf(stderr, "File format options:\n");
     fprintf(stderr, "   -o, --output <file>             write output to a file [standard output]\n");
     fprintf(stderr, "   -O, --output-type <b|u|z|v>     output type: 'b' compressed BCF; 'u' uncompressed BCF; 'z' compressed VCF; 'v' uncompressed VCF [v]\n");
+    fprintf(stderr, "       --ploidy <assembly>[?]      predefined ploidy, 'list' to print available settings, append '?' for details\n");
+    fprintf(stderr, "       --ploidy-file <file>        space/tab-delimited list of CHROM,FROM,TO,SEX,PLOIDY\n");
     fprintf(stderr, "   -r, --regions <region>          restrict to comma-separated list of regions\n");
     fprintf(stderr, "   -R, --regions-file <file>       restrict to regions listed in a file\n");
     fprintf(stderr, "   -s, --samples <list>            list of samples to include [all samples]\n");
-    fprintf(stderr, "   -S, --samples-file <file>       PED file or a file with optional second column for ploidy (0, 1 or 2) [all samples]\n");
+    fprintf(stderr, "   -S, --samples-file <file>       PED file or a file with an optional column with sex (see man page for details) [all samples]\n");
     fprintf(stderr, "   -t, --targets <region>          similar to -r but streams rather than index-jumps\n");
     fprintf(stderr, "   -T, --targets-file <file>       similar to -R but streams rather than index-jumps\n");
+    fprintf(stderr, "       --threads <int>             number of extra output compression threads [0]\n");
     fprintf(stderr, "\n");
     fprintf(stderr, "Input/output options:\n");
     fprintf(stderr, "   -A, --keep-alts                 keep all possible alternate alleles at variant sites\n");
     fprintf(stderr, "   -f, --format-fields <list>      output format fields: GQ,GP (lowercase allowed) []\n");
-    fprintf(stderr, "   -g, --gvcf <minDP>              output gVCF blocks of homozygous REF calls\n");
+    fprintf(stderr, "   -g, --gvcf <int>,[...]          group non-variant sites into gVCF blocks by minimum per-sample DP\n");
     fprintf(stderr, "   -i, --insert-missed             output also sites missed by mpileup but present in -T\n");
     fprintf(stderr, "   -M, --keep-masked-ref           keep sites with masked reference allele (REF=N)\n");
     fprintf(stderr, "   -V, --skip-variants <type>      skip indels/snps\n");
@@ -488,8 +607,6 @@ static void usage(args_t *args)
     fprintf(stderr, "   -n, --novel-rate <float>,[...]  likelihood of novel mutation for constrained trio calling, see man page for details [1e-8,1e-9,1e-9]\n");
     fprintf(stderr, "   -p, --pval-threshold <float>    variant if P(ref|D)<FLOAT with -c [0.5]\n");
     fprintf(stderr, "   -P, --prior <float>             mutation rate (use bigger for greater sensitivity) [1.1e-3]\n");
-    fprintf(stderr, "   -X, --chromosome-X              haploid output for male samples (requires PED file with -s)\n");
-    fprintf(stderr, "   -Y, --chromosome-Y              haploid output for males and skips females (requires PED file with -s)\n");
 
     // todo (and more)
     // fprintf(stderr, "\nContrast calling and association test options:\n");
@@ -503,7 +620,7 @@ static void usage(args_t *args)
 
 int main_vcfcall(int argc, char *argv[])
 {
-    char *samples_fname = NULL;
+    char *ploidy_fname = NULL, *ploidy = NULL;
     args_t args;
     memset(&args, 0, sizeof(args_t));
     args.argc = argc; args.argv = argv;
@@ -516,51 +633,53 @@ int main_vcfcall(int argc, char *argv[])
     args.flag           = CF_ACGT_ONLY;
     args.output_fname   = "-";
     args.output_type    = FT_VCF;
+    args.n_threads = 0;
     args.aux.trio_Pm_SNPs = 1 - 1e-8;
     args.aux.trio_Pm_ins  = args.aux.trio_Pm_del  = 1 - 1e-9;
 
-    int i, c, samples_is_file = 0;
-
+    int c;
     static struct option loptions[] =
     {
-        {"help",0,0,'h'},
-        {"gvcf",1,0,'g'},
-        {"format-fields",1,0,'f'},
-        {"output",1,0,'o'},
-        {"output-type",1,0,'O'},
-        {"regions",1,0,'r'},
-        {"regions-file",1,0,'R'},
-        {"samples",1,0,'s'},
-        {"samples-file",1,0,'S'},
-        {"targets",1,0,'t'},
-        {"targets-file",1,0,'T'},
-        {"keep-alts",0,0,'A'},
-        {"insert-missed",0,0,'i'},
-        {"skip-Ns",0,0,'N'},            // now the new default
-        {"keep-masked-refs",0,0,'M'},
-        {"skip-variants",1,0,'V'},
-        {"variants-only",0,0,'v'},
-        {"consensus-caller",0,0,'c'},
-        {"constrain",1,0,'C'},
-        {"multiallelic-caller",0,0,'m'},
-        {"pval-threshold",1,0,'p'},
-        {"prior",1,0,'P'},
-        {"chromosome-X",0,0,'X'},
-        {"chromosome-Y",0,0,'Y'},
-        {"novel-rate",1,0,'n'},
-        {0,0,0,0}
+        {"help",no_argument,NULL,'h'},
+        {"format-fields",required_argument,NULL,'f'},
+        {"gvcf",required_argument,NULL,'g'},
+        {"output",required_argument,NULL,'o'},
+        {"output-type",required_argument,NULL,'O'},
+        {"regions",required_argument,NULL,'r'},
+        {"regions-file",required_argument,NULL,'R'},
+        {"samples",required_argument,NULL,'s'},
+        {"samples-file",required_argument,NULL,'S'},
+        {"targets",required_argument,NULL,'t'},
+        {"targets-file",required_argument,NULL,'T'},
+        {"threads",required_argument,NULL,9},
+        {"keep-alts",no_argument,NULL,'A'},
+        {"insert-missed",no_argument,NULL,'i'},
+        {"skip-Ns",no_argument,NULL,'N'},            // now the new default
+        {"keep-masked-refs",no_argument,NULL,'M'},
+        {"skip-variants",required_argument,NULL,'V'},
+        {"variants-only",no_argument,NULL,'v'},
+        {"consensus-caller",no_argument,NULL,'c'},
+        {"constrain",required_argument,NULL,'C'},
+        {"multiallelic-caller",no_argument,NULL,'m'},
+        {"pval-threshold",required_argument,NULL,'p'},
+        {"prior",required_argument,NULL,'P'},
+        {"novel-rate",required_argument,NULL,'n'},
+        {"ploidy",required_argument,NULL,1},
+        {"ploidy-file",required_argument,NULL,2},
+        {"chromosome-X",no_argument,NULL,'X'},
+        {"chromosome-Y",no_argument,NULL,'Y'},
+        {NULL,0,NULL,0}
     };
 
     char *tmp = NULL;
-    while ((c = getopt_long(argc, argv, "h?o:O:r:R:s:S:t:T:ANMV:vcmp:C:XYn:P:f:ig:", loptions, NULL)) >= 0)
+    while ((c = getopt_long(argc, argv, "h?o:O:r:R:s:S:t:T:ANMV:vcmp:C:n:P:f:ig:XY", loptions, NULL)) >= 0)
     {
         switch (c)
         {
-            case 'g':
-                args.flag |= CF_GVCF;
-                args.gvcf.min_dp = strtol(optarg,&tmp,10);
-                if ( *tmp ) error("Could not parse, expected integer argument: -g %s\n", optarg);
-                break;
+            case  2 : ploidy_fname = optarg; break;
+            case  1 : ploidy = optarg; break;
+            case 'X': ploidy = "X"; fprintf(stderr,"Warning: -X will be deprecated, please use --ploidy instead.\n"); break;
+            case 'Y': ploidy = "Y"; fprintf(stderr,"Warning: -Y will be deprecated, please use --ploidy instead.\n"); break;
             case 'f': args.aux.output_tags |= parse_format_flag(optarg); break;
             case 'M': args.flag &= ~CF_ACGT_ONLY; break;     // keep sites where REF is N
             case 'N': args.flag |= CF_ACGT_ONLY; break;      // omit sites where first base in REF is N (the new default)
@@ -568,6 +687,10 @@ int main_vcfcall(int argc, char *argv[])
             case 'c': args.flag |= CF_CCALL; break;          // the original EM based calling method
             case 'i': args.flag |= CF_INS_MISSED; break;
             case 'v': args.aux.flag |= CALL_VARONLY; break;
+            case 'g': 
+                args.gvcf = gvcf_init(optarg);
+                if ( !args.gvcf ) error("Could not parse: --gvcf %s\n", optarg);
+                break;
             case 'o': args.output_fname = optarg; break;
             case 'O':
                       switch (optarg[0]) {
@@ -583,8 +706,6 @@ int main_vcfcall(int argc, char *argv[])
                       else if ( !strcasecmp(optarg,"trio") ) args.aux.flag |= CALL_CONSTR_TRIO;
                       else error("Unknown argument to -C: \"%s\"\n", optarg);
                       break;
-            case 'X': args.aux.flag |= CALL_CHR_X; break;
-            case 'Y': args.aux.flag |= CALL_CHR_Y; break;
             case 'V':
                       if ( !strcasecmp(optarg,"snps") ) args.flag |= CF_INDEL_ONLY;
                       else if ( !strcasecmp(optarg,"indels") ) args.flag |= CF_NO_INDEL;
@@ -603,11 +724,16 @@ int main_vcfcall(int argc, char *argv[])
             case 'R': args.regions = optarg; args.regions_is_file = 1; break;
             case 't': args.targets = optarg; break;
             case 'T': args.targets = optarg; args.targets_is_file = 1; break;
-            case 's': samples_fname = optarg; break;
-            case 'S': samples_fname = optarg; samples_is_file = 1; break;
+            case 's': args.samples_fname = optarg; break;
+            case 'S': args.samples_fname = optarg; args.samples_is_file = 1; break;
+            case  9 : args.n_threads = strtol(optarg, 0, 0); break;
             default: usage(&args);
         }
     }
+    // Sanity check options and initialize
+    if ( ploidy_fname ) args.ploidy = ploidy_init(ploidy_fname, 2);
+    else if ( ploidy ) args.ploidy = init_ploidy(ploidy);
+
     if ( optind>=argc )
     {
         if ( !isatty(fileno((FILE *)stdin)) ) args.bcf_fname = "-";  // reading from stdin
@@ -615,34 +741,24 @@ int main_vcfcall(int argc, char *argv[])
     }
     else args.bcf_fname = argv[optind++];
 
-    // Sanity check options and initialize
-    if ( samples_fname )
-    {
-        args.samples = read_samples(&args.aux, samples_fname, samples_is_file, &args.nsamples);
-        args.aux.ploidy = (uint8_t*) calloc(args.nsamples+1, 1);
-        args.aux.all_diploid = 1;
-        for (i=0; i<args.nsamples; i++)
-        {
-            args.aux.ploidy[i] = args.samples[i][strlen(args.samples[i]) + 1];
-            if ( args.aux.ploidy[i]!=2 ) args.aux.all_diploid = 0;
-        }
-    }
-    if ( args.flag & CF_GVCF )
+    if ( !ploidy_fname && !ploidy )
     {
-        // Force some flags to avoid unnecessary branching
-        args.aux.flag &= ~CALL_KEEPALT;
-        args.aux.flag |= CALL_VARONLY;
+        fprintf(stderr,"Note: Neither --ploidy nor --ploidy-file given, assuming all sites are diploid\n");
+        args.ploidy = ploidy_init_string("",2);
     }
+
+    if ( !args.ploidy ) error("Could not initialize ploidy\n");
     if ( (args.flag & CF_CCALL ? 1 : 0) + (args.flag & CF_MCALL ? 1 : 0) + (args.flag & CF_QCALL ? 1 : 0) > 1 ) error("Only one of -c or -m options can be given\n");
     if ( !(args.flag & CF_CCALL) && !(args.flag & CF_MCALL) && !(args.flag & CF_QCALL) ) error("Expected -c or -m option\n");
+    if ( (args.flag & CF_CCALL ? 1: 0) && args.gvcf ) error("gvcf -g option not functional with -c calling mode yet\n");
     if ( args.aux.n_perm && args.aux.ngrp1_samples<=0 ) error("Expected -1 with -U\n");    // not sure about this, please fix
     if ( args.aux.flag & CALL_CONSTR_ALLELES )
     {
         if ( !args.targets ) error("Expected -t or -T with \"-C alleles\"\n");
         if ( !(args.flag & CF_MCALL) ) error("The \"-C alleles\" mode requires -m\n");
     }
-    if ( args.aux.flag & CALL_CHR_X && args.aux.flag & CALL_CHR_Y ) error("Only one of -X or -Y should be given\n");
     if ( args.flag & CF_INS_MISSED && !(args.aux.flag&CALL_CONSTR_ALLELES) ) error("The -i option requires -C alleles\n");
+    if ( args.aux.flag&CALL_VARONLY && args.gvcf ) error("The two options cannot be combined: --variants-only and --gvcf\n");
     init_data(&args);
 
     while ( bcf_sr_next_line(args.aux.srs) )
@@ -652,29 +768,29 @@ int main_vcfcall(int argc, char *argv[])
         bcf_unpack(bcf_rec, BCF_UN_STR);
 
         // Skip unwanted sites
-        if ( args.aux.flag & CALL_VARONLY )
+        int i, is_indel = bcf_is_snp(bcf_rec) ? 0 : 1;
+        if ( (args.flag & CF_INDEL_ONLY) && !is_indel ) continue;
+        if ( (args.flag & CF_NO_INDEL) && is_indel ) continue;
+        if ( (args.flag & CF_ACGT_ONLY) && (bcf_rec->d.allele[0][0]=='N' || bcf_rec->d.allele[0][0]=='n') ) continue;   // REF[0] is 'N'
+
+        // Which allele is symbolic? All SNPs should have it, but not indels
+        args.aux.unseen = 0;
+        for (i=1; i<bcf_rec->n_allele; i++)
         {
-            int is_ref = 0;
-            if ( bcf_rec->n_allele==1 ) is_ref = 1;     // not a variant
-            else if ( bcf_rec->n_allele==2 )
+            if ( bcf_rec->d.allele[i][0]=='X' ) { args.aux.unseen = i; break; }  // old X
+            if ( bcf_rec->d.allele[i][0]=='<' )
             {
-                // second allele is mpileup's X, not a variant
-                if ( bcf_rec->d.allele[1][0]=='X' ) is_ref = 1;
-                else if ( bcf_rec->d.allele[1][0]=='<' && bcf_rec->d.allele[1][1]=='X' && bcf_rec->d.allele[1][2]=='>' ) is_ref = 1;
-                else if ( bcf_rec->d.allele[1][0]=='<' && bcf_rec->d.allele[1][1]=='*' && bcf_rec->d.allele[1][2]=='>' ) is_ref = 1;
-            }
-            if ( is_ref )
-            {
-                // gVCF output
-                if ( args.flag & CF_GVCF ) gvcf_write(args.out_fh, &args.gvcf, args.aux.hdr, bcf_rec, 1);
-                continue;
+                if ( bcf_rec->d.allele[i][1]=='X' && bcf_rec->d.allele[i][2]=='>' ) { args.aux.unseen = i; break; } // old <X>
+                if ( bcf_rec->d.allele[i][1]=='*' && bcf_rec->d.allele[i][2]=='>' ) { args.aux.unseen = i; break; } // new <*>
             }
         }
-        if ( (args.flag & CF_INDEL_ONLY) && bcf_is_snp(bcf_rec) ) continue;    // not an indel
-        if ( (args.flag & CF_NO_INDEL) && !bcf_is_snp(bcf_rec) ) continue;     // not a SNP
-        if ( (args.flag & CF_ACGT_ONLY) && (bcf_rec->d.allele[0][0]=='N' || bcf_rec->d.allele[0][0]=='n') ) continue;   // REF[0] is 'N'
+        int is_ref = (bcf_rec->n_allele==1 || (bcf_rec->n_allele==2 && args.aux.unseen>0)) ? 1 : 0;
+
+        if ( is_ref && args.aux.flag&CALL_VARONLY )
+            continue;
 
         bcf_unpack(bcf_rec, BCF_UN_ALL);
+        if ( args.nsex ) set_ploidy(&args, bcf_rec);
 
         // Various output modes: QCall output (todo)
         if ( args.flag & CF_QCALL )
@@ -691,18 +807,14 @@ int main_vcfcall(int argc, char *argv[])
             ret = ccall(&args.aux, bcf_rec);
         if ( ret==-1 ) error("Something is wrong\n");
 
-        // gVCF output
-        if ( args.flag & CF_GVCF )
-        {
-            gvcf_write(args.out_fh, &args.gvcf, args.aux.hdr, bcf_rec, ret?0:1);
-            continue;
-        }
-
         // Normal output
-        if ( (args.aux.flag & CALL_VARONLY) && ret==0 ) continue;     // not a variant
-        bcf_write1(args.out_fh, args.aux.hdr, bcf_rec);
+        if ( (args.aux.flag & CALL_VARONLY) && ret==0 && !args.gvcf ) continue;     // not a variant
+        if ( args.gvcf )
+            bcf_rec = gvcf_write(args.gvcf, args.out_fh, args.aux.hdr, bcf_rec, ret==1?1:0);
+        if ( bcf_rec )
+            bcf_write1(args.out_fh, args.aux.hdr, bcf_rec);
     }
-    if ( args.flag & CF_GVCF ) gvcf_write(args.out_fh, &args.gvcf, args.aux.hdr, NULL, 0);
+    if ( args.gvcf ) gvcf_write(args.gvcf, args.out_fh, args.aux.hdr, NULL, 0);
     if ( args.flag & CF_INS_MISSED ) bcf_sr_regions_flush(args.aux.srs->targets);
     destroy_data(&args);
     return 0;
diff --git a/vcfcnv.c b/vcfcnv.c
index 7011795..e4b9372 100644
--- a/vcfcnv.c
+++ b/vcfcnv.c
@@ -1,6 +1,6 @@
 /* The MIT License
 
-   Copyright (c) 2014 Genome Research Ltd.
+   Copyright (c) 2014-2015 Genome Research Ltd.
 
    Author: Petr Danecek <pd3 at sanger.ac.uk>
    
@@ -24,6 +24,12 @@
 
  */
 
+/*
+    Known issues:
+    - The --AF-file option behaves like --targets-file, sites not listed in the AFs
+      are skipped.
+*/
+
 #include <stdio.h>
 #include <unistd.h>
 #include <getopt.h>
@@ -35,20 +41,29 @@
 #include <htslib/khash_str2int.h>
 #include "bcftools.h"
 #include "HMM.h"
+#include "rbuf.h"
 
-#define DBG_HMM_PRN 0
+#define DBG0 0
 
-#define N_STATES 5
+#define N_STATES 4
 #define CN0 0
 #define CN1 1
 #define CN2 2
 #define CN3 3
-#define CNx 4
+
+typedef struct
+{
+    float mean, dev2, norm;
+}
+gauss_param_t;
 
 typedef struct
 {
     char *name;
-    int idx;
+    int idx;    // VCF sample index
+    float *lrr,*baf, baf_dev2, baf_dev2_dflt, lrr_dev2;
+    float cell_frac, cell_frac_dflt;
+    gauss_param_t gauss_param[18];
     double pobs[N_STATES];
     FILE *dat_fh, *cn_fh, *summary_fh;
     char *dat_fname, *cn_fname, *summary_fname;
@@ -63,13 +78,15 @@ typedef struct _args_t
     sample_t query_sample, control_sample;
 
     int nstates;    // number of states: N_STATES for one sample, N_STATES^2 for two samples
-    double baf_sigma2, lrr_sigma2;          // squared std dev of B-allele frequency and LRR distribution
     double lrr_bias, baf_bias;              // LRR/BAF weights
     double same_prob, ij_prob;              // prior of both samples being the same and the transition probability P(i|j)
     double err_prob;                        // constant probability of erroneous measurement
-    double pRR, pRA, pAA, pRR_dflt, pRA_dflt, pAA_dflt;
+    float *nonref_afs, nonref_af, nonref_af_dflt, fRR, fRA, fAA, *tmpf;
+    unsigned long int nRR, nRA, nAA;
+    int mtmpf;
 
     double *tprob, *tprob_arr;  // array of transition matrices, precalculated up to ntprob_arr positions
+    double *iprobs;             // states' initial probabilities
     int ntprob_arr;
 
     hmm_t *hmm;
@@ -77,18 +94,17 @@ typedef struct _args_t
     uint32_t *sites;        // positions [nsites,msites]
     int nsites, msites;
 
-    double baum_welch_th;
+    double baum_welch_th, optimize_frac; 
     float plot_th;
     FILE *summary_fh;
     char **argv, *regions_list, *summary_fname, *output_dir;
     char *targets_list, *af_fname;
-    int argc;
+    int argc, verbose, lrr_smooth_win;
 }
 args_t;
 
 FILE *open_file(char **fname, const char *mode, const char *fmt, ...);
 
-
 static inline void hmm2cn_state(int nstates, int i, int *a, int *b)
 {
     *a = i / N_STATES;
@@ -100,10 +116,10 @@ static double *init_tprob_matrix(int ndim, double ij_prob, double same_prob)
     double *mat = (double*) malloc(sizeof(double)*ndim*ndim);
 
     assert( ndim==N_STATES || ndim==N_STATES*N_STATES);
-    double pii = 1 - ij_prob*(N_STATES-1);
 
     if ( ndim==N_STATES )   // one sample
     {
+        double pii = 1 - ij_prob*(N_STATES-1);
         if ( pii < ij_prob ) error("Error: -x set a bit too high, P(x|x) < P(x|y): %e vs %e\n", pii,ij_prob);
         for (j=0; j<ndim; j++)
         {
@@ -115,6 +131,7 @@ static double *init_tprob_matrix(int ndim, double ij_prob, double same_prob)
                     MAT(mat,ndim,i,j) = pii;
                 else
                     MAT(mat,ndim,i,j) = ij_prob;
+
                 sum += MAT(mat,ndim,i,j);
             }
             assert( fabs(sum - 1.0)<1e-15 );
@@ -122,6 +139,11 @@ static double *init_tprob_matrix(int ndim, double ij_prob, double same_prob)
     }
     else    // two samples
     {
+        // interpret ij_prob differently, as ii_prob in fact, so that for two
+        // samples the behaviour is somewhat closer to single sample calling
+        // with s=0. 
+        double pii = 1 - ij_prob*(N_STATES-1);
+        ij_prob = (1 - pii) / (ndim - 1);
         for (j=0; j<ndim; j++)
         {
             int ja,jb;
@@ -152,14 +174,49 @@ static double *init_tprob_matrix(int ndim, double ij_prob, double same_prob)
     return mat;
 }
 
+static double *init_iprobs(int ndim, double same_prob)
+{
+    int i;
+    double *probs = (double*) malloc(sizeof(double)*ndim);
+
+    assert( ndim==N_STATES || ndim==N_STATES*N_STATES);
+
+    if ( ndim==N_STATES )   
+    {
+        // one sample: prior on CN2
+        for (i=0; i<ndim; i++) 
+            probs[i] = i==CN2 ? 0.5 : 0.5/3;
+    }
+    else
+    {
+        // two samples
+        double norm = 0;
+        for (i=0; i<ndim; i++) 
+        {
+            int ia,ib;
+            hmm2cn_state(ndim, i, &ia, &ib);
+
+            double pa = ia==CN2 ? 0.5 : 0.5/3;
+            double pb = ib==CN2 ? 0.5 : 0.5/3;
+
+            probs[i] = pa*pb;
+            if ( ia!=ib ) probs[i] *= 1-same_prob;
+
+            norm += probs[i];
+        }
+        for (i=0; i<ndim; i++) probs[i] /= norm;
+    }
+    return probs;
+}
+
 static void init_sample_files(sample_t *smpl, char *dir)
 {
     smpl->dat_fh = open_file(&smpl->dat_fname,"w","%s/dat.%s.tab",dir,smpl->name);
     smpl->cn_fh  = open_file(&smpl->cn_fname,"w","%s/cn.%s.tab",dir,smpl->name);
     smpl->summary_fh = open_file(&smpl->summary_fname,"w","%s/summary.%s.tab",dir,smpl->name);
     fprintf(smpl->dat_fh,"# [1]Chromosome\t[2]Position\t[3]BAF\t[4]LRR\n");
-    fprintf(smpl->cn_fh,"# [1]Chromosome\t[2]Position\t[3]CN\t[4]P(CN0)\t[5]P(CN1)\t[6]P(CN2)\t[7]P(CN3)\t[8]P(CNx)\n");
-    fprintf(smpl->summary_fh,"# RG, Regions [2]Chromosome\t[3]Start\t[4]End\t[5]Copy Number state\t[6]Quality\n");
+    fprintf(smpl->cn_fh,"# [1]Chromosome\t[2]Position\t[3]CN\t[4]P(CN0)\t[5]P(CN1)\t[6]P(CN2)\t[7]P(CN3)\n");
+    fprintf(smpl->summary_fh,"# RG, Regions [2]Chromosome\t[3]Start\t[4]End\t[5]Copy Number state\t[6]Quality\t[7]nSites\t[8]nHETs\n");
 }
 static void close_sample_files(sample_t *smpl)
 {
@@ -168,6 +225,7 @@ static void close_sample_files(sample_t *smpl)
     fclose(smpl->summary_fh);
 }
 
+static double norm_cdf(double mean, double dev);
 static void init_data(args_t *args)
 {
     args->prev_rid = -1;
@@ -202,8 +260,10 @@ static void init_data(args_t *args)
     args->query_sample.idx = bcf_hdr_id2int(args->hdr,BCF_DT_SAMPLE,args->query_sample.name);
     args->control_sample.idx = args->control_sample.name ? bcf_hdr_id2int(args->hdr,BCF_DT_SAMPLE,args->control_sample.name) : -1;
     args->nstates = args->control_sample.name ? N_STATES*N_STATES : N_STATES;
-    args->tprob = init_tprob_matrix(args->nstates, args->ij_prob, args->same_prob);
+    args->tprob  = init_tprob_matrix(args->nstates, args->ij_prob, args->same_prob);
+    args->iprobs = init_iprobs(args->nstates, args->same_prob);
     args->hmm = hmm_init(args->nstates, args->tprob, 10000);
+    hmm_init_states(args->hmm, args->iprobs);
 
     args->summary_fh = stdout;
     if ( args->output_dir )
@@ -226,12 +286,13 @@ static void init_data(args_t *args)
     for (i=1; i<args->argc; i++) fprintf(fh, " %s",args->argv[i]);
     if ( args->control_sample.name )
         fprintf(fh, "\n#\n"
-                "# RG, Regions\t[2]Chromosome\t[3]Start\t[4]End\t[5]Copy number:%s\t[6]Copy number:%s\t[7]Quality\n",
+                "# RG, Regions\t[2]Chromosome\t[3]Start\t[4]End\t[5]Copy number:%s\t[6]Copy number:%s\t[7]Quality"
+                "\t[8]nSites in (5)\t[9]nHETs in (5)\t[10]nSites in (6)\t[11]nHETs in(6)\n",
                 args->query_sample.name,args->control_sample.name
                );
     else
         fprintf(fh, "\n#\n"
-                "# RG, Regions\t[2]Chromosome\t[3]Start\t[4]End\t[5]Copy number:%s\t[6]Quality\n",
+                "# RG, Regions\t[2]Chromosome\t[3]Start\t[4]End\t[5]Copy number:%s\t[6]Quality\t[7]nSites\t[8]nHETs\n",
                 args->query_sample.name
                );
 }
@@ -292,7 +353,6 @@ static void plot_sample(args_t *args, sample_t *smpl)
             "       heat[1][x] = cn_dat[x][3]\n"
             "       heat[2][x] = cn_dat[x][4]\n"
             "       heat[3][x] = cn_dat[x][5]\n"
-            "       heat[4][x] = cn_dat[x][6]\n"
             "    mesh = ax3.pcolormesh(xgrid, ygrid, heat, cmap='bwr_r')\n"
             "    mesh.set_clim(vmin=-1,vmax=1)\n"
             "    ax3.plot([x[0] for x in cn_dat],[x[1] for x in cn_dat],'.-',ms=3,color='black')\n"
@@ -304,9 +364,9 @@ static void plot_sample(args_t *args, sample_t *smpl)
             "    ax2.set_ylabel('BAF')\n"
             "    ax3.set_ylabel('CN')\n"
             "    ax3.set_xlabel('Coordinate (chrom '+chr+')',fontsize=10)\n"
-            "    ax3.set_ylim(-0.1,5.1)\n"
-            "    ax3.set_yticks([0.5,1.5,2.5,3.5,4.5])\n"
-            "    ax3.set_yticklabels(['CN0','CN1','CN2','CN3','CN4'])\n"
+            "    ax3.set_ylim(-0.1,4.1)\n"
+            "    ax3.set_yticks([0.5,1.5,2.5,3.5])\n"
+            "    ax3.set_yticklabels(['CN0','CN1','CN2','CN3'])\n"
             "    plt.subplots_adjust(left=0.08,right=0.95,bottom=0.08,top=0.92)\n"
             "    plt.savefig('%s/plot.%s.chr'+chr+'.png')\n"
             "    plt.close()\n"
@@ -373,24 +433,21 @@ static void create_plots(args_t *args)
             "else:\n"
             "   plot_chroms = chroms_to_plot(args.plot_threshold)\n"
             "\n"
-            "def read_dat(file,dat):\n"
+            "def read_dat(file,dat,plot_chr):\n"
             "   with open(file, 'rb') as f:\n"
             "       reader = csv.reader(f, 'tab')\n"
             "       for row in reader:\n"
             "           chr = row[0]\n"
-            "           if chr[0]=='#': continue\n"
-            "           if chr not in plot_chroms: continue\n"
-            "           if chr not in dat: dat[chr] = []\n"
-            "           dat[chr].append([row[1], float(row[2]), float(row[3])])\n"
-            "def read_cnv(file,cnv):\n"
+            "           if chr != plot_chr: continue\n"
+            "           dat.append([row[1], float(row[2]), float(row[3])])\n"
+            "def read_cnv(file,cnv,plot_chr):\n"
             "   with open(file, 'rb') as f:\n"
             "       reader = csv.reader(f, 'tab')\n"
             "       for row in reader:\n"
             "           chr = row[0]\n"
-            "           if chr[0]=='#': continue\n"
-            "           if chr not in cnv: cnv[chr] = []\n"
+            "           if chr != plot_chr: continue\n"
             "           row[2] = int(row[2]) + 0.5\n"
-            "           cnv[chr].append(row[1:])\n"
+            "           cnv.append(row[1:])\n"
             "def find_diffs(a,b):\n"
             "    out = []\n"
             "    diff = []\n"
@@ -405,20 +462,20 @@ static void create_plots(args_t *args)
             "    if len(diff): out.append(diff)\n"
             "    return out\n"
             "\n"
-            "control_dat = {}\n"
-            "control_cnv = {}\n"
-            "query_dat   = {}\n"
-            "query_cnv   = {}\n"
-            "read_dat('%s',control_dat)\n"
-            "read_dat('%s',query_dat)\n"
-            "read_cnv('%s',control_cnv)\n"
-            "read_cnv('%s',query_cnv)\n"
+            "for chr in sorted(plot_chroms.keys()):\n"
+            "    control_dat = []\n"
+            "    control_cnv = []\n"
+            "    query_dat   = []\n"
+            "    query_cnv   = []\n"
+            "    read_dat('%s',control_dat,chr)\n"
+            "    read_dat('%s',query_dat,chr)\n"
+            "    read_cnv('%s',control_cnv,chr)\n"
+            "    read_cnv('%s',query_cnv,chr)\n"
             "\n"
-            "for chr in query_dat:\n"
             "    fig,(ax1,ax2,ax3,ax4,ax5,ax6) = plt.subplots(6,1,figsize=(10,8),sharex=True)\n"
-            "    ax1.plot([x[0] for x in control_dat[chr]],[x[2] for x in control_dat[chr]], '.', ms=3,color='red')\n"
-            "    ax2.plot([x[0] for x in control_dat[chr]],[x[1] for x in control_dat[chr]], '.', ms=3,color='red')\n"
-            "    cn_dat = control_cnv[chr]\n"
+            "    ax1.plot([x[0] for x in control_dat],[x[2] for x in control_dat], '.', ms=3,color='red')\n"
+            "    ax2.plot([x[0] for x in control_dat],[x[1] for x in control_dat], '.', ms=3,color='red')\n"
+            "    cn_dat = control_cnv\n"
             "    xgrid = [float(x[0]) for x in cn_dat]\n"
             "    ygrid = np.linspace(0,5,6)\n"
             "    xgrid, ygrid = np.meshgrid(xgrid, ygrid)\n"
@@ -428,14 +485,13 @@ static void create_plots(args_t *args)
             "       heat[1][x] = cn_dat[x][3]\n"
             "       heat[2][x] = cn_dat[x][4]\n"
             "       heat[3][x] = cn_dat[x][5]\n"
-            "       heat[4][x] = cn_dat[x][6]\n"
             "    mesh = ax3.pcolormesh(xgrid, ygrid, heat, cmap='bwr')\n"
             "    mesh.set_clim(vmin=-1,vmax=1)\n"
             "    ax3.plot([x[0] for x in cn_dat],[x[1] for x in cn_dat],'-',ms=3,color='black',lw=1.7)\n"
             "\n"
-            "    ax6.plot([x[0] for x in query_dat[chr]],[x[2] for x in query_dat[chr]], '.', ms=3)\n"
-            "    ax5.plot([x[0] for x in query_dat[chr]],[x[1] for x in query_dat[chr]], '.', ms=3)\n"
-            "    cn_dat = query_cnv[chr]\n"
+            "    ax6.plot([x[0] for x in query_dat],[x[2] for x in query_dat], '.', ms=3)\n"
+            "    ax5.plot([x[0] for x in query_dat],[x[1] for x in query_dat], '.', ms=3)\n"
+            "    cn_dat = query_cnv\n"
             "    xgrid = [float(x[0]) for x in cn_dat]\n"
             "    ygrid = np.linspace(0,5,6)\n"
             "    xgrid, ygrid = np.meshgrid(xgrid, ygrid)\n"
@@ -445,14 +501,13 @@ static void create_plots(args_t *args)
             "       heat[1][x] = cn_dat[x][3]\n"
             "       heat[2][x] = cn_dat[x][4]\n"
             "       heat[3][x] = cn_dat[x][5]\n"
-            "       heat[4][x] = cn_dat[x][6]\n"
             "    mesh = ax4.pcolormesh(xgrid, ygrid, heat, cmap='bwr_r')\n"
             "    mesh.set_clim(vmin=-1,vmax=1)\n"
             "    ax4.plot([x[0] for x in cn_dat],[x[1] for x in cn_dat],'-',ms=3,color='black',lw=1.7)\n"
             "    ax3.annotate(control_sample, xy=(0.02,0.1), xycoords='axes fraction', color='red',fontsize=12, va='bottom',ha='left')\n"
             "    ax4.annotate(query_sample, xy=(0.02,0.9), xycoords='axes fraction', color='blue',fontsize=12, va='top',ha='left')\n"
             "\n"
-            "    diffs = find_diffs(control_cnv[chr],query_cnv[chr])\n"
+            "    diffs = find_diffs(control_cnv,query_cnv)\n"
             "    for diff in diffs:\n"
             "        ax3.plot([x[0] for x in diff],[x[1] for x in diff],'-',ms=3,color='blue',lw=1.7)\n"
             "        ax4.plot([x[0] for x in diff],[x[2] for x in diff],'-',ms=3,color='red',lw=1.7)\n"
@@ -471,12 +526,12 @@ static void create_plots(args_t *args)
             "    ax6.set_ylabel('LRR')\n"
             "    ax5.set_ylabel('BAF')\n"
             "    ax4.set_ylabel('CN')\n"
-            "    ax3.set_ylim(-0.1,5.1)\n"
-            "    ax3.set_yticks([0.5,1.5,2.5,3.5,4.5])\n"
-            "    ax3.set_yticklabels(['CN0','CN1','CN2','CN3','CN4'])\n"
-            "    ax4.set_ylim(-0.1,5.1)\n"
-            "    ax4.set_yticks([0.5,1.5,2.5,3.5,4.5])\n"
-            "    ax4.set_yticklabels(['CN0','CN1','CN2','CN3','CN4'])\n"
+            "    ax3.set_ylim(-0.1,4.1)\n"
+            "    ax3.set_yticks([0.5,1.5,2.5,3.5])\n"
+            "    ax3.set_yticklabels(['CN0','CN1','CN2','CN3'])\n"
+            "    ax4.set_ylim(-0.1,4.1)\n"
+            "    ax4.set_yticks([0.5,1.5,2.5,3.5])\n"
+            "    ax4.set_yticklabels(['CN0','CN1','CN2','CN3'])\n"
             "    plt.subplots_adjust(left=0.08,right=0.95,bottom=0.08,top=0.92,hspace=0)\n"
             "    plt.savefig('%s/plot.%s.%s.chr'+chr+'.png')\n"
             "    plt.close()\n"
@@ -497,10 +552,16 @@ static void destroy_data(args_t *args)
 {
     bcf_sr_destroy(args->files);
     hmm_destroy(args->hmm);
+    free(args->tmpf);
     free(args->sites);
     free(args->eprob);
     free(args->tprob);
     free(args->summary_fname);
+    free(args->nonref_afs);
+    free(args->query_sample.baf);
+    free(args->query_sample.lrr);
+    free(args->control_sample.baf);
+    free(args->control_sample.lrr);
     free(args->query_sample.name);
     free(args->query_sample.dat_fname);
     free(args->query_sample.cn_fname);
@@ -518,13 +579,6 @@ static inline char copy_number_state(args_t *args, int istate, int ismpl)
     return code[idx];
 }
 
-static double phred_score(double prob)
-{
-    if ( prob==0 ) return 99;
-    prob = -4.3429*log(prob);
-    return prob>99 ? 99 : prob;
-}
-
 static double avg_ii_prob(int n, double *mat)
 {
     int i;
@@ -533,29 +587,401 @@ static double avg_ii_prob(int n, double *mat)
     return avg/n;
 }
 
+#define GAUSS_CN1_PK_R(smpl)    (&((smpl)->gauss_param[0]))
+#define GAUSS_CN1_PK_A(smpl)    (&((smpl)->gauss_param[1]))
+#define GAUSS_CN2_PK_RR(smpl)   (&((smpl)->gauss_param[2]))
+#define GAUSS_CN2_PK_RA(smpl)   (&((smpl)->gauss_param[3]))
+#define GAUSS_CN2_PK_AA(smpl)   (&((smpl)->gauss_param[4]))
+#define GAUSS_CN3_PK_RRR(smpl)  (&((smpl)->gauss_param[5]))
+#define GAUSS_CN3_PK_RRA(smpl)  (&((smpl)->gauss_param[6]))
+#define GAUSS_CN3_PK_RAA(smpl)  (&((smpl)->gauss_param[7]))
+#define GAUSS_CN3_PK_AAA(smpl)  (&((smpl)->gauss_param[8]))
+
+static inline double norm_prob(double baf, gauss_param_t *param)
+{
+    return exp(-(baf-param->mean)*(baf-param->mean)*0.5/param->dev2) / param->norm / sqrt(2*M_PI*param->dev2);
+}
+
+static int set_observed_prob(args_t *args, sample_t *smpl, int isite)
+{
+    float baf = smpl->baf[isite];
+    float lrr = args->lrr_bias>0 ? smpl->lrr[isite] : 0;
+
+    float fRR = args->fRR;
+    float fRA = args->fRA;
+    float fAA = args->fAA;
+
+    if ( baf<0 )
+    {
+        // no call: either some technical issue or the call could not be made because it is CN0
+        int i;
+        smpl->pobs[CN0] = 0.5;
+        for (i=1; i<N_STATES; i++) smpl->pobs[i] = (1.0-smpl->pobs[CN0])/(N_STATES-1);
+        return 0;
+    }
+
+    double cn1_baf = 
+        norm_prob(baf,GAUSS_CN1_PK_R(smpl)) * (fRR + fRA*0.5) +
+        norm_prob(baf,GAUSS_CN1_PK_A(smpl)) * (fAA + fRA*0.5) ;
+    double cn2_baf = 
+        norm_prob(baf,GAUSS_CN2_PK_RR(smpl)) * fRR + 
+        norm_prob(baf,GAUSS_CN2_PK_RA(smpl)) * fRA + 
+        norm_prob(baf,GAUSS_CN2_PK_AA(smpl)) * fAA;
+    double cn3_baf = 
+        norm_prob(baf,GAUSS_CN3_PK_RRR(smpl)) * fRR + 
+        norm_prob(baf,GAUSS_CN3_PK_RRA(smpl)) * fRA*0.5 + 
+        norm_prob(baf,GAUSS_CN3_PK_RAA(smpl)) * fRA*0.5 + 
+        norm_prob(baf,GAUSS_CN3_PK_AAA(smpl)) * fAA;
+
+    double norm = cn1_baf + cn2_baf + cn3_baf;
+    cn1_baf /= norm;
+    cn2_baf /= norm;
+    cn3_baf /= norm;
+
+    #if DBG0
+    if ( args->verbose ) fprintf(stderr,"%f\t%f %f %f\n", baf,cn1_baf,cn2_baf,cn3_baf);
+    #endif
+
+    double cn1_lrr = exp(-(lrr + 0.45)*(lrr + 0.45)/smpl->lrr_dev2);
+    double cn2_lrr = exp(-(lrr - 0.00)*(lrr - 0.00)/smpl->lrr_dev2);
+    double cn3_lrr = exp(-(lrr - 0.30)*(lrr - 0.30)/smpl->lrr_dev2);
+
+    smpl->pobs[CN0] = 0;
+    smpl->pobs[CN1] = args->err_prob + (1 - args->baf_bias + args->baf_bias*cn1_baf)*(1 - args->lrr_bias + args->lrr_bias*cn1_lrr);
+    smpl->pobs[CN2] = args->err_prob + (1 - args->baf_bias + args->baf_bias*cn2_baf)*(1 - args->lrr_bias + args->lrr_bias*cn2_lrr);
+    smpl->pobs[CN3] = args->err_prob + (1 - args->baf_bias + args->baf_bias*cn3_baf)*(1 - args->lrr_bias + args->lrr_bias*cn3_lrr);
+
+    return 0;
+}
+
+static void set_emission_prob(args_t *args, int isite)
+{
+    double *eprob = &args->eprob[args->nstates*isite];
+    int i;
+    for (i=0; i<N_STATES; i++)
+        eprob[i] = args->query_sample.pobs[i];
+}
+
+static void set_emission_prob2(args_t *args, int isite)
+{
+    double *eprob = &args->eprob[args->nstates*isite];
+    int i, j;
+    for (i=0; i<N_STATES; i++)
+    {
+        for (j=0; j<N_STATES; j++)
+        {
+            eprob[i*N_STATES+j] = args->query_sample.pobs[i]*args->control_sample.pobs[j];
+        }
+    }
+}
+
+static void set_gauss_params(args_t *args, sample_t *smpl);
+static double norm_cdf(double mean, double dev)
+{
+    double bot = 0, top = 1;
+    top = 1 - 0.5*erfc((top-mean)/(dev*sqrt(2)));
+    bot = 1 - 0.5*erfc((bot-mean)/(dev*sqrt(2)));
+    return top-bot;
+}
+
+static void set_emission_probs(args_t *args)
+{
+    if ( !args->af_fname )
+    {
+        args->fRR = 0.76;
+        args->fRA = 0.14;
+        args->fAA = 0.098;
+    }
+
+    set_gauss_params(args, &args->query_sample);
+    if ( args->control_sample.name ) set_gauss_params(args, &args->control_sample);
+
+    #if DBG0
+    args->verbose = 1;
+    args->query_sample.baf[0] = 0; set_observed_prob(args,&args->query_sample,0);
+    args->query_sample.baf[0] = 1/3.; set_observed_prob(args,&args->query_sample,0);
+    args->query_sample.baf[0] = 1/2.; set_observed_prob(args,&args->query_sample,0);
+    args->query_sample.baf[0] = 2/3.; set_observed_prob(args,&args->query_sample,0);
+    args->query_sample.baf[0] = 1; set_observed_prob(args,&args->query_sample,0);
+    args->verbose = 0;
+    #endif
+
+    int i;
+    for (i=0; i<args->nsites; i++)
+    {
+        if ( args->af_fname )
+        {
+            args->fRR = (1-args->nonref_afs[i])*(1-args->nonref_afs[i]);
+            args->fRA = 2*args->nonref_afs[i]*(1-args->nonref_afs[i]);
+            args->fAA = args->nonref_afs[i]*args->nonref_afs[i];
+        }
+        set_observed_prob(args,&args->query_sample,i);
+        if ( args->control_sample.name )
+        {
+            set_observed_prob(args,&args->control_sample,i);
+            set_emission_prob2(args,i);
+        }
+        else
+            set_emission_prob(args,i);
+    }
+}
+
+static void smooth_data(float *dat, int ndat, int win)
+{
+    if ( win<=1 ) return;
+
+    int i,j, k1 = win/2, k2 = win-k1;
+    rbuf_t rbuf;
+    rbuf_init(&rbuf,win);
+    float sum = 0, *buf = (float*)malloc(sizeof(float)*win);
+    for (i=0; i<k2; i++)
+    {
+        sum += dat[i];
+        int j = rbuf_append(&rbuf);
+        buf[j] = dat[i];
+    }
+    for (i=0; i<ndat; i++)
+    {
+        dat[i] = sum/rbuf.n;
+        if ( i>=k1 )
+        {
+            j = rbuf_shift(&rbuf);
+            sum -= buf[j];
+        }
+        if ( i+k2<ndat )
+        {
+            sum += dat[i+k2];
+            j = rbuf_append(&rbuf);
+            buf[j] = dat[i+k2];
+        }
+    }
+    free(buf);
+}
+
+static void set_gauss_params(args_t *args, sample_t *smpl)
+{
+    int i;
+    for (i=0; i<18; i++) smpl->gauss_param[i].dev2 = smpl->baf_dev2;
+
+    double dev = sqrt(smpl->baf_dev2);
+
+    GAUSS_CN1_PK_R(smpl)->mean = 0;
+    GAUSS_CN1_PK_A(smpl)->mean = 1;
+    GAUSS_CN1_PK_R(smpl)->norm = norm_cdf(GAUSS_CN1_PK_R(smpl)->mean,dev);
+    GAUSS_CN1_PK_A(smpl)->norm = norm_cdf(GAUSS_CN1_PK_A(smpl)->mean,dev);
+
+    GAUSS_CN2_PK_RR(smpl)->mean = 0;
+    GAUSS_CN2_PK_RA(smpl)->mean = 0.5;
+    GAUSS_CN2_PK_AA(smpl)->mean = 1;
+    GAUSS_CN2_PK_RR(smpl)->norm = norm_cdf(GAUSS_CN2_PK_RR(smpl)->mean,dev);
+    GAUSS_CN2_PK_RA(smpl)->norm = norm_cdf(GAUSS_CN2_PK_RA(smpl)->mean,dev);
+    GAUSS_CN2_PK_AA(smpl)->norm = norm_cdf(GAUSS_CN2_PK_AA(smpl)->mean,dev);
+
+    GAUSS_CN3_PK_RRR(smpl)->mean = 0;
+    GAUSS_CN3_PK_RRA(smpl)->mean = 1.0/(2+smpl->cell_frac);
+    GAUSS_CN3_PK_RAA(smpl)->mean = (1.0+smpl->cell_frac)/(2+smpl->cell_frac);
+    GAUSS_CN3_PK_AAA(smpl)->mean = 1;
+    GAUSS_CN3_PK_RRR(smpl)->norm = norm_cdf(GAUSS_CN3_PK_RRR(smpl)->mean,dev);
+    GAUSS_CN3_PK_RRA(smpl)->norm = norm_cdf(GAUSS_CN3_PK_RRA(smpl)->mean,dev);
+    GAUSS_CN3_PK_RAA(smpl)->norm = norm_cdf(GAUSS_CN3_PK_RAA(smpl)->mean,dev);
+    GAUSS_CN3_PK_AAA(smpl)->norm = norm_cdf(GAUSS_CN3_PK_AAA(smpl)->mean,dev);
+}
+
+static int update_sample_args(args_t *args, sample_t *smpl, int ismpl)
+{
+    hmm_t *hmm = args->hmm;
+    double *fwd = hmm_get_fwd_bwd_prob(hmm);
+    int nstates = hmm_get_nstates(hmm);
+
+    // estimate the BAF mean and deviation for CN3
+    double mean_cn3 = 0, norm_cn3 = 0;
+    double baf_dev2 = 0, baf_AA_dev2 = 0, norm_baf_AA_dev2 = 0;
+
+    // experimental: smooth CN3 probs to bias toward bigger events, this lowers
+    // the FP rate when the data is noisy
+    hts_expand(float,args->nsites,args->mtmpf,args->tmpf);
+    int i, j, k = 0;
+    for (i=0; i<args->nsites; i++)
+    {
+        float baf = smpl->baf[i];
+        if ( baf>4/5.) continue;        // skip AA genotypes
+        if ( baf>0.5 ) baf = 1 - baf;   // the bands should be symmetric
+        if ( baf<1/5.) continue;        // skip RR genotypes
+
+        double prob_cn3 = 0, *probs = fwd + i*nstates;
+        if ( !args->control_sample.name )
+        {
+            prob_cn3 = probs[CN3];
+        }
+        else if ( ismpl==0 )
+        {
+            // query sample: CN3 probability must be recovered from all states of the control sample
+            for (j=0; j<N_STATES; j++) prob_cn3 += probs[CN3*N_STATES+j];
+        }
+        else
+        {
+            // same as above but for control sample
+            for (j=0; j<N_STATES; j++) prob_cn3 += probs[CN3+j*N_STATES];
+        }
+        args->tmpf[k++] = prob_cn3;
+    }
+    smooth_data(args->tmpf, k, 50);
+    k = 0;
+    for (i=0; i<args->nsites; i++)
+    {
+        float baf = smpl->baf[i];
+        if ( baf>4/5.) { baf_AA_dev2 += (1.0-baf)*(1.0-baf); norm_baf_AA_dev2++; continue; }       // skip AA genotypes
+        if ( baf>0.5 ) baf = 1 - baf;   // the bands should be symmetric
+        if ( baf<1/5.) continue;        // skip RR genotypes
+
+        double prob_cn3 = args->tmpf[k++];
+        mean_cn3 += prob_cn3 * baf;
+        norm_cn3 += prob_cn3;
+    }
+    if ( !norm_cn3 )
+    {
+        smpl->cell_frac = 1.0;
+        return 1;
+    }
+    mean_cn3 /= norm_cn3;
+    k = 0;
+    for (i=0; i<args->nsites; i++)
+    {
+        float baf = smpl->baf[i];
+        if ( baf>0.5 ) baf = 1 - baf;   // the bands should be symmetric
+        if ( baf<1/5.) continue;        // skip RR,AA genotypes
+
+        double prob_cn3 = args->tmpf[k++];
+        baf_dev2 += prob_cn3 * (baf - mean_cn3)*(baf - mean_cn3);
+    }
+
+    /*
+        A noisy CN2 band is hard to distinguish from two CN3 bands which are
+        close to each other. Set a treshold on the minimum separation based
+        on the BAF deviation at p=0.95
+    */
+    baf_dev2 /= norm_cn3;
+    baf_AA_dev2 /= norm_baf_AA_dev2;
+    if ( baf_dev2 < baf_AA_dev2 )  baf_dev2 = baf_AA_dev2;
+    double max_mean_cn3 = 0.5 - sqrt(baf_dev2)*1.644854;    // R: qnorm(0.95)=1.644854
+    //fprintf(stderr,"dev=%f  AA_dev=%f  max_mean_cn3=%f  mean_cn3=%f\n", baf_dev2,baf_AA_dev2,max_mean_cn3,mean_cn3);
+    assert( max_mean_cn3>0 );
+
+    double new_frac = 1./mean_cn3 - 2;
+    if ( mean_cn3 > max_mean_cn3 || new_frac < args->optimize_frac )
+    {
+        // out of bounds, beyond our detection limits. Give up and say it converged
+        smpl->cell_frac = 1.0;
+        return 1;
+    }
+    if ( new_frac>1 ) new_frac = 1;
+    int converged = fabs(new_frac - smpl->cell_frac) < 1e-1 ? 1 : 0;
+
+    // Update dev2, but stay within safe limits
+    if ( baf_dev2 > 3*smpl->baf_dev2_dflt ) baf_dev2 = 3*smpl->baf_dev2_dflt;
+    else if ( baf_dev2 < 0.5*smpl->baf_dev2_dflt ) baf_dev2 = 0.5*smpl->baf_dev2_dflt;
+
+    smpl->cell_frac = new_frac;
+    smpl->baf_dev2  = baf_dev2;
+
+    return converged;
+}
+
+// Update parameters which depend on the estimated fraction of aberrant cells
+// in CN3.  Returns 0 if the current estimate did not need to be updated or 1
+// if there was a change.
+static int update_args(args_t *args)
+{
+    int converged = update_sample_args(args, &args->query_sample, 0);
+    if ( args->control_sample.name )
+    {
+        converged += update_sample_args(args, &args->control_sample, 1);
+        return converged==2 ? 0 : 1;
+    }
+    return converged ? 0 : 1;
+}
+
+// for an approximate estimate of the number of het genotypes in a region
+#define BAF_LIKELY_HET(val)   (val)>0.25 && (val)<0.75
+
 static void cnv_flush_viterbi(args_t *args)
 {
     if ( !args->nsites ) return;
 
+    // Set HMM transition matrix for the new chromsome again. This is for case
+    // Baum-Welch was used, which is experimental, largerly unsupported and not
+    // done by default.
     hmm_t *hmm = args->hmm;
     hmm_set_tprob(args->hmm, args->tprob, 10000);
+
+    // Smooth LRR values to reduce noise
+    if ( args->lrr_bias > 0 )
+    {
+        smooth_data(args->query_sample.lrr,args->nsites, args->lrr_smooth_win);
+        if ( args->control_sample.name ) smooth_data(args->control_sample.lrr,args->nsites, args->lrr_smooth_win);
+    }
+
+    // Set the BAF peak likelihoods, such as P(RRR|CN3), taking account the
+    // estimated fraction of aberrant cells in the mixture. With the new chromosome,
+    // reset the fraction to the default value.
+    args->query_sample.cell_frac   = args->query_sample.cell_frac_dflt;
+    args->control_sample.cell_frac = args->control_sample.cell_frac_dflt;
+    args->query_sample.baf_dev2    = args->query_sample.baf_dev2_dflt;
+    args->control_sample.baf_dev2  = args->control_sample.baf_dev2_dflt;
+    set_gauss_params(args, &args->query_sample);
+    if ( args->control_sample.name ) set_gauss_params(args, &args->control_sample);
+
+    if ( args->optimize_frac )
+    {
+        int niter = 0;
+        fprintf(stderr,"Attempting to estimate the fraction of aberrant cells (chr %s):\n", bcf_hdr_id2name(args->hdr,args->prev_rid));
+        do
+        {
+            fprintf(stderr,"\t.. %f %f", args->query_sample.cell_frac,args->query_sample.baf_dev2);
+            if ( args->control_sample.name )
+                fprintf(stderr,"\t.. %f %f", args->control_sample.cell_frac,args->control_sample.baf_dev2);
+            fprintf(stderr,"\n");
+            set_emission_probs(args);
+            hmm_run_fwd_bwd(hmm, args->nsites, args->eprob, args->sites);
+        }
+        while ( update_args(args) && ++niter<20 );
+        if ( niter>=20 )
+        {
+            // no convergence
+            args->query_sample.cell_frac   = args->query_sample.cell_frac_dflt;
+            args->control_sample.cell_frac = args->control_sample.cell_frac_dflt;
+            args->query_sample.baf_dev2    = args->query_sample.baf_dev2_dflt;
+            args->control_sample.baf_dev2  = args->control_sample.baf_dev2_dflt;
+            set_gauss_params(args, &args->query_sample);
+            if ( args->control_sample.name ) set_gauss_params(args, &args->control_sample);
+        }
+
+        fprintf(stderr,"\t.. %f %f", args->query_sample.cell_frac,args->query_sample.baf_dev2);
+        if ( args->control_sample.name )
+            fprintf(stderr,"\t.. %f %f", args->control_sample.cell_frac,args->control_sample.baf_dev2);
+        fprintf(stderr,"\n");
+    }
+    set_emission_probs(args);
+
     while ( args->baum_welch_th!=0 )
     {
-        double ori_ii = avg_ii_prob(hmm->nstates,hmm->tprob_arr);
+        int nstates = hmm_get_nstates(hmm);
+        double ori_ii = avg_ii_prob(nstates,hmm_get_tprob(hmm));
         hmm_run_baum_welch(hmm, args->nsites, args->eprob, args->sites);
-        double new_ii = avg_ii_prob(hmm->nstates,hmm->tprob_arr);
+        double new_ii = avg_ii_prob(nstates,hmm_get_tprob(hmm));
         fprintf(stderr,"%e\t%e\t%e\n", ori_ii,new_ii,new_ii-ori_ii);
-        double *tprob = init_tprob_matrix(hmm->nstates, 1-new_ii, args->same_prob);
+        double *tprob = init_tprob_matrix(nstates, 1-new_ii, args->same_prob);
         hmm_set_tprob(args->hmm, tprob, 10000);
+        double *tprob_arr = hmm_get_tprob(hmm);
         free(tprob);
         if ( fabs(new_ii - ori_ii) < args->baum_welch_th )
         {
             int i,j;
-            for (i=0; i<hmm->nstates; i++)
+            for (i=0; i<nstates; i++)
             {
-                for (j=0; j<hmm->nstates; j++)
+                for (j=0; j<nstates; j++)
                 {
-                    printf(" %.15f", MAT(hmm->tprob_arr,hmm->nstates,j,i));
+                    printf(" %.15f", MAT(tprob_arr,nstates,j,i));
                 }
                 printf("\n");
             }
@@ -567,12 +993,14 @@ static void cnv_flush_viterbi(args_t *args)
 
 
     // Output the results
-    double qual = 0;
-    int i,j, isite, start_cn = hmm->vpath[0], start_pos = args->sites[0], istart_pos = 0;
+    uint8_t *vpath = hmm_get_viterbi_path(hmm);
+    double qual = 0, *fwd = hmm_get_fwd_bwd_prob(hmm);
+    int i,j, isite, start_cn = vpath[0], start_pos = args->sites[0], istart_pos = 0;
+    int ctrl_ntot = 0, smpl_ntot = 0, ctrl_nhet = 0, smpl_nhet = 0;
     for (isite=0; isite<args->nsites; isite++)
     {
-        int state = hmm->vpath[args->nstates*isite];
-        double *pval = hmm->fwd + isite*args->nstates;
+        int state = vpath[args->nstates*isite];
+        double *pval = fwd + isite*args->nstates;
 
         qual += pval[start_cn];
 
@@ -590,6 +1018,11 @@ static void cnv_flush_viterbi(args_t *args)
                     fprintf(args->query_sample.cn_fh, "\t%f", sum);
                 }
             fprintf(args->query_sample.cn_fh, "\n");
+            if ( args->query_sample.baf[isite]>=0 )     // if non-missing
+            {
+                if ( BAF_LIKELY_HET(args->query_sample.baf[isite]) ) smpl_nhet++;
+                smpl_ntot++;
+            }
         }
         if ( args->control_sample.cn_fh )
         {
@@ -601,109 +1034,65 @@ static void cnv_flush_viterbi(args_t *args)
                 fprintf(args->control_sample.cn_fh, "\t%f", sum);
             }
             fprintf(args->control_sample.cn_fh, "\n");
+            if ( args->control_sample.baf[isite]>=0 )     // if non-missing
+            {
+                if ( BAF_LIKELY_HET(args->control_sample.baf[isite]) ) ctrl_nhet++;
+                ctrl_ntot++;
+            }
         }
 
         if ( start_cn != state )
         {
             char start_cn_query = copy_number_state(args,start_cn,0);
             qual = phred_score(1 - qual/(isite - istart_pos));
-            fprintf(args->query_sample.summary_fh,"RG\t%s\t%d\t%d\t%c\t%.1f\n",bcf_hdr_id2name(args->hdr,args->prev_rid), start_pos+1, args->sites[isite],start_cn_query,qual);
+            fprintf(args->query_sample.summary_fh,"RG\t%s\t%d\t%d\t%c\t%.1f\t%d\t%d\n",
+                bcf_hdr_id2name(args->hdr,args->prev_rid), start_pos+1, args->sites[isite],start_cn_query,qual,smpl_ntot,smpl_nhet);
 
             if ( args->control_sample.name )
             {
                 // regions 0-based, half-open
                 char start_cn_ctrl = copy_number_state(args,start_cn,1);
-                fprintf(args->control_sample.summary_fh,"RG\t%s\t%d\t%d\t%c\t%.1f\n",bcf_hdr_id2name(args->hdr,args->prev_rid), start_pos+1, args->sites[isite],start_cn_ctrl,qual);
-                fprintf(args->summary_fh,"RG\t%s\t%d\t%d\t%c\t%c\t%.1f\n",bcf_hdr_id2name(args->hdr,args->prev_rid), start_pos+1, args->sites[isite],start_cn_query,start_cn_ctrl,qual);
+                fprintf(args->control_sample.summary_fh,"RG\t%s\t%d\t%d\t%c\t%.1f\t%d\t%d\n",
+                    bcf_hdr_id2name(args->hdr,args->prev_rid), start_pos+1, args->sites[isite],start_cn_ctrl,qual,ctrl_ntot,ctrl_nhet);
+                fprintf(args->summary_fh,"RG\t%s\t%d\t%d\t%c\t%c\t%.1f\t%d\t%d\t%d\t%d\n",
+                    bcf_hdr_id2name(args->hdr,args->prev_rid), start_pos+1, args->sites[isite],start_cn_query,start_cn_ctrl,qual,smpl_ntot,smpl_nhet,ctrl_ntot,ctrl_nhet);
             }
 
             istart_pos = isite;
             start_pos = args->sites[isite];
             start_cn = state;
             qual = 0;
+            smpl_ntot = smpl_nhet = ctrl_ntot = ctrl_nhet = 0;
         }
     }
     qual = phred_score(1 - qual/(isite - istart_pos));
     char start_cn_query = copy_number_state(args,start_cn,0);
-    fprintf(args->query_sample.summary_fh,"RG\t%s\t%d\t%d\t%c\t%.1f\n",bcf_hdr_id2name(args->hdr,args->prev_rid), start_pos+1, args->sites[isite-1]+1,start_cn_query,qual);
+    fprintf(args->query_sample.summary_fh,"RG\t%s\t%d\t%d\t%c\t%.1f\t%d\t%d\n",
+        bcf_hdr_id2name(args->hdr,args->prev_rid), start_pos+1, args->sites[isite-1]+1,start_cn_query,qual,smpl_ntot,smpl_nhet);
     if ( args->control_sample.name )
     {
         char start_cn_ctrl = copy_number_state(args,start_cn,1);
-        fprintf(args->control_sample.summary_fh,"RG\t%s\t%d\t%d\t%c\t%.1f\n",bcf_hdr_id2name(args->hdr,args->prev_rid), start_pos+1, args->sites[isite-1]+1,start_cn_ctrl,qual);
-        fprintf(args->summary_fh,"RG\t%s\t%d\t%d\t%c\t%c\t%.1f\n",bcf_hdr_id2name(args->hdr,args->prev_rid), start_pos+1, args->sites[isite-1]+1,start_cn_query,start_cn_ctrl,qual);
+        fprintf(args->control_sample.summary_fh,"RG\t%s\t%d\t%d\t%c\t%.1f\t%d\t%d\n",
+            bcf_hdr_id2name(args->hdr,args->prev_rid), start_pos+1, args->sites[isite-1]+1,start_cn_ctrl,qual,ctrl_ntot,ctrl_nhet);
+        fprintf(args->summary_fh,"RG\t%s\t%d\t%d\t%c\t%c\t%.1f\t%d\t%d\t%d\t%d\n",
+            bcf_hdr_id2name(args->hdr,args->prev_rid), start_pos+1, args->sites[isite-1]+1,start_cn_query,start_cn_ctrl,qual,smpl_ntot,smpl_nhet,ctrl_ntot,ctrl_nhet);
     }
 }
 
-static int set_observed_prob(args_t *args, bcf_fmt_t *baf_fmt, bcf_fmt_t *lrr_fmt, sample_t *smpl)
+static int parse_lrr_baf(sample_t *smpl, bcf_fmt_t *baf_fmt, bcf_fmt_t *lrr_fmt, float *baf, float *lrr)
 {
-    float baf, lrr;
-    baf = ((float*)(baf_fmt->p + baf_fmt->size*smpl->idx))[0];
-    if ( bcf_float_is_missing(baf) || isnan(baf) ) baf = -0.1;    // arbitrary negative value == missing value
+    *baf = ((float*)(baf_fmt->p + baf_fmt->size*smpl->idx))[0];
+    if ( bcf_float_is_missing(*baf) || isnan(*baf) ) *baf = -0.1;    // arbitrary negative value == missing value
 
-    lrr = ((float*)(lrr_fmt->p + lrr_fmt->size*smpl->idx))[0];
-    if ( bcf_float_is_missing(lrr) || isnan(lrr) ) baf = -0.1;
-
-    if ( baf>=0 )    // skip missing values
-        fprintf(smpl->dat_fh,"%s\t%d\t%.3f\t%.3f\n",bcf_hdr_id2name(args->hdr,args->prev_rid), args->sites[args->nsites-1]+1,baf,lrr);
-
-    if ( baf<0 )
+    if ( lrr_fmt )
     {
-        // no call: either some technical issue or the call could not be made because it is CN0
-        int i;
-        smpl->pobs[CN0] = 0.5;
-        for (i=1; i<N_STATES; i++) smpl->pobs[i] = (1.0-smpl->pobs[CN0])/(N_STATES-1);
-        return 0;
+        *lrr = ((float*)(lrr_fmt->p + lrr_fmt->size*smpl->idx))[0];
+        if ( bcf_float_is_missing(*lrr) || isnan(*lrr) ) { *lrr = 0; *baf = -0.1; }
     }
+    else
+        *lrr = 0;
 
-    double pk0, pk14, pk13, pk12, pk23, pk34, pk1;
-    pk0  = exp(-baf*baf/args->baf_sigma2);
-    pk14 = exp(-(baf-1/4.)*(baf-1/4.)/args->baf_sigma2);
-    pk13 = exp(-(baf-1/3.)*(baf-1/3.)/args->baf_sigma2);
-    pk12 = exp(-(baf-1/2.)*(baf-1/2.)/args->baf_sigma2);
-    pk23 = exp(-(baf-2/3.)*(baf-2/3.)/args->baf_sigma2);
-    pk34 = exp(-(baf-3/4.)*(baf-3/4.)/args->baf_sigma2);
-    pk1  = exp(-(baf-1.0)*(baf-1.0)/args->baf_sigma2);
-
-    double cn1_baf, cn2_baf, cn3_baf, cn4_baf;
-    cn1_baf = pk0*(args->pRR+args->pRA/2.)  + pk1*(args->pAA+args->pRA/2.);
-    cn2_baf = pk0*args->pRR + pk1*args->pAA + pk12*args->pRA;
-    cn3_baf = pk0*args->pRR + pk1*args->pAA + (pk13 + pk23)*args->pRA/2.;
-    cn4_baf = pk0*args->pRR + pk1*args->pAA + (pk14 + pk12 + pk34)*args->pRA/3.;
-
-    double cn1_lrr, cn2_lrr, cn3_lrr, cn4_lrr;
-    cn1_lrr = exp(-(lrr + 0.45)*(lrr + 0.45)/args->lrr_sigma2);
-    cn2_lrr = exp(-(lrr - 0.00)*(lrr - 0.00)/args->lrr_sigma2);
-    cn3_lrr = exp(-(lrr - 0.30)*(lrr - 0.30)/args->lrr_sigma2);
-    cn4_lrr = exp(-(lrr - 0.75)*(lrr - 0.75)/args->lrr_sigma2);
-
-    smpl->pobs[CN0] = 0;
-    smpl->pobs[CN1] = args->err_prob + (1 - args->baf_bias + args->baf_bias*cn1_baf)*(1 - args->lrr_bias + args->lrr_bias*cn1_lrr);
-    smpl->pobs[CN2] = args->err_prob + (1 - args->baf_bias + args->baf_bias*cn2_baf)*(1 - args->lrr_bias + args->lrr_bias*cn2_lrr);
-    smpl->pobs[CN3] = args->err_prob + (1 - args->baf_bias + args->baf_bias*cn3_baf)*(1 - args->lrr_bias + args->lrr_bias*cn3_lrr);
-    smpl->pobs[CNx] = args->err_prob + (1 - args->baf_bias + args->baf_bias*cn4_baf)*(1 - args->lrr_bias + args->lrr_bias*cn4_lrr);
-
-    return 0;
-}
-
-static void set_emission_prob(args_t *args)
-{
-    double *eprob = &args->eprob[args->nstates*(args->nsites-1)];
-    int i;
-    for (i=0; i<N_STATES; i++)
-        eprob[i] = args->query_sample.pobs[i];
-}
-
-static void set_emission_prob2(args_t *args)
-{
-    double *eprob = &args->eprob[args->nstates*(args->nsites-1)];
-    int i, j;
-    for (i=0; i<N_STATES; i++)
-    {
-        for (j=0; j<N_STATES; j++)
-        {
-            eprob[i*N_STATES+j] = args->query_sample.pobs[i]*args->control_sample.pobs[j];
-        }
-    }
+    return *baf<0 ? 0 : 1;
 }
 
 int read_AF(bcf_sr_regions_t *tgt, bcf1_t *line, double *alt_freq);
@@ -723,58 +1112,63 @@ static void cnv_next_line(args_t *args, bcf1_t *line)
         cnv_flush_viterbi(args);
         args->prev_rid = line->rid;
         args->nsites = 0;
+        args->nRR = args->nAA = args->nRA = 0;
     }
 
     // Process line
     args->ntot++;
 
-    bcf_fmt_t *baf_fmt, *lrr_fmt;
+    bcf_fmt_t *baf_fmt, *lrr_fmt = NULL;
     if ( !(baf_fmt = bcf_get_fmt(args->hdr, line, "BAF")) ) return; 
-    if ( !(lrr_fmt = bcf_get_fmt(args->hdr, line, "LRR")) ) return;
+    if ( args->lrr_bias>0 && !(lrr_fmt = bcf_get_fmt(args->hdr, line, "LRR")) ) return;
 
-    // Realloc buffers needed by viterbi and fwd-bwd
+    float baf1,lrr1,baf2,lrr2;
+    int ret = 0;
+    ret += parse_lrr_baf(&args->query_sample,  baf_fmt,lrr_fmt,&baf1,&lrr1);
+    ret += parse_lrr_baf(&args->control_sample,baf_fmt,lrr_fmt,&baf2,&lrr2);
+    if ( !ret ) return;
+
+    // Realloc buffers needed to store observed data and used by viterbi and fwd-bwd
     args->nsites++;
     int m = args->msites;
     hts_expand(uint32_t,args->nsites,args->msites,args->sites);
     if ( args->msites!=m )
+    {
         args->eprob = (double*) realloc(args->eprob,sizeof(double)*args->msites*args->nstates);
+        if ( args->control_sample.name )
+        {
+            args->control_sample.lrr = (float*) realloc(args->control_sample.lrr,sizeof(float)*args->msites);
+            args->control_sample.baf = (float*) realloc(args->control_sample.baf,sizeof(float)*args->msites);
+        }
+        args->query_sample.lrr = (float*) realloc(args->query_sample.lrr,sizeof(float)*args->msites);
+        args->query_sample.baf = (float*) realloc(args->query_sample.baf,sizeof(float)*args->msites);
+        if ( args->af_fname )
+            args->nonref_afs = (float*) realloc(args->nonref_afs,sizeof(float)*args->msites);
+    }
     args->sites[args->nsites-1] = line->pos;
-
-    double alt_freq;
-    if ( !args->af_fname || read_AF(args->files->targets, line, &alt_freq) < 0 )
+    args->query_sample.lrr[args->nsites-1] = lrr1;
+    args->query_sample.baf[args->nsites-1] = baf1;
+    if ( args->af_fname )
     {
-        args->pRR = args->pRR_dflt;
-        args->pRA = args->pRA_dflt;
-        args->pAA = args->pAA_dflt;
+        double alt_freq;
+        args->nonref_afs[args->nsites-1] = read_AF(args->files->targets,line,&alt_freq)<0 ? args->nonref_af_dflt : alt_freq;
     }
-    else
+    if ( args->control_sample.name )
     {
-        args->pRR = (1 - alt_freq)*(1 - alt_freq);
-        args->pRA = 2*(1 - alt_freq)*alt_freq;
-        args->pAA = alt_freq*alt_freq;
+        args->control_sample.lrr[args->nsites-1] = lrr2;
+        args->control_sample.baf[args->nsites-1] = baf2;
+        if ( baf2>=0 )  // skip missing values
+            fprintf(args->control_sample.dat_fh,"%s\t%d\t%.3f\t%.3f\n",bcf_hdr_id2name(args->hdr,args->prev_rid), line->pos+1,baf2,lrr2);
     }
+    if ( baf1>=0 )  // skip missing values
+        fprintf(args->query_sample.dat_fh,"%s\t%d\t%.3f\t%.3f\n",bcf_hdr_id2name(args->hdr,args->prev_rid), line->pos+1,baf1,lrr1);
 
-    int ret = set_observed_prob(args, baf_fmt,lrr_fmt, &args->query_sample);
-    if ( ret<0 ) 
-    {
-        args->nsites--;
-        return;
-    }
-    if ( args->control_sample.name )
+    if ( baf1>=0 )
     {
-        ret = set_observed_prob(args, baf_fmt,lrr_fmt, &args->control_sample);
-        if ( ret<0 )
-        {
-            args->nsites--;
-            return;
-        }
+        if ( baf1<1/5. ) args->nRR++;
+        else if ( baf1>4/5. ) args->nAA++;
+        else args->nRA++;
     }
-
-    if ( args->control_sample.name )
-        set_emission_prob2(args);
-    else
-        set_emission_prob(args);
-
     args->nused++;
 }
 
@@ -783,7 +1177,7 @@ static void usage(args_t *args)
     fprintf(stderr, "\n");
     fprintf(stderr, "About:   Copy number variation caller, requires Illumina's B-allele frequency (BAF) and Log R\n");
     fprintf(stderr, "         Ratio intensity (LRR). The HMM considers the following copy number states: CN 2\n");
-    fprintf(stderr, "         (normal), 1 (single-copy loss), 0 (complete loss), 3 (single-copy gain), x (other)\n");
+    fprintf(stderr, "         (normal), 1 (single-copy loss), 0 (complete loss), 3 (single-copy gain)\n");
     fprintf(stderr, "Usage:   bcftools cnv [OPTIONS] <file.vcf>\n");
     fprintf(stderr, "General Options:\n");
     fprintf(stderr, "    -c, --control-sample <string>      optional control sample name to highlight differences\n");
@@ -796,11 +1190,16 @@ static void usage(args_t *args)
     fprintf(stderr, "    -t, --targets <region>             similar to -r but streams rather than index-jumps\n");
     fprintf(stderr, "    -T, --targets-file <file>          similar to -R but streams rather than index-jumps\n");
     fprintf(stderr, "HMM Options:\n");
+    fprintf(stderr, "    -a, --aberrant <float[,float]>     fraction of aberrant cells in query and control [1.0,1.0]\n");
     fprintf(stderr, "    -b, --BAF-weight <float>           relative contribution from BAF [1]\n");
-    fprintf(stderr, "    -e, --err-prob <float>             probability of error [1e-4]\n");
+    fprintf(stderr, "    -d, --BAF-dev <float[,float]>      expected BAF deviation in query and control [0.04,0.04]\n"); // experimental
+    fprintf(stderr, "    -e, --err-prob <float>             uniform error probability [1e-4]\n");
+    fprintf(stderr, "    -k, --LRR-dev <float[,float]>      expected LRR deviation [0.2,0.2]\n"); // experimental
     fprintf(stderr, "    -l, --LRR-weight <float>           relative contribution from LRR [0.2]\n");
-    fprintf(stderr, "    -P, --same-prob <float>            prior probability of -s/-c being same [1e-1]\n");
-    fprintf(stderr, "    -x, --xy-prob <float>              P(x|y) transition probability [1e-8]\n");
+    fprintf(stderr, "    -L, --LRR-smooth-win <int>         window of LRR moving average smoothing [10]\n");
+    fprintf(stderr, "    -O, --optimize <float>             estimate fraction of aberrant cells down to <float> [1.0]\n");
+    fprintf(stderr, "    -P, --same-prob <float>            prior probability of -s/-c being the same [0.5]\n");
+    fprintf(stderr, "    -x, --xy-prob <float>              P(x|y) transition probability [1e-9]\n");
     fprintf(stderr, "\n");
     exit(1);
 }
@@ -812,6 +1211,11 @@ int main_vcfcnv(int argc, char *argv[])
     args->argc      = argc; args->argv = argv;
     args->files     = bcf_sr_init();
     args->plot_th   = 1e9;   // by default plot none
+    args->nonref_af_dflt = 0.1;
+    args->lrr_smooth_win = 10;
+
+    args->query_sample.cell_frac_dflt = 1;
+    args->control_sample.cell_frac_dflt = 1;
 
     // How much FORMAT/LRR and FORMAT/BAF matter
     args->lrr_bias  = 0.2;
@@ -819,26 +1223,23 @@ int main_vcfcnv(int argc, char *argv[])
     args->err_prob  = 1e-4;
 
     // Transition probability to a different state and the prior of both samples being the same
-    args->ij_prob   = 1e-8;
-    args->same_prob = 1e-1;
+    args->ij_prob   = 1e-9;
+    args->same_prob = 0.5;
 
     // Squared std dev of BAF and LRR values (gaussian noise), estimated from real data (hets, one sample, one chr)
-    args->baf_sigma2 = 0.08*0.08;   // illumina: 0.03
-    args->lrr_sigma2 = 0.4*0.4; //0.20*0.20;   // illumina: 0.18
-
-    // Priors for RR, RA, AA genotypes
-    args->pRR_dflt = 0.76;
-    args->pRA_dflt = 0.14;
-    args->pAA_dflt = 0.098;
-    // args->pRR = 0.69;
-    // args->pRA = 0.18;
-    // args->pAA = 0.11;
+    args->query_sample.baf_dev2_dflt = args->control_sample.baf_dev2_dflt = 0.04*0.04; // illumina: 0.03
+    args->query_sample.lrr_dev2 = args->control_sample.lrr_dev2 = 0.2*0.2; //0.20*0.20;   // illumina: 0.18
 
     int regions_is_file = 0, targets_is_file = 0;
     static struct option loptions[] = 
     {
+        {"BAF-dev",1,0,'d'},
+        {"LRR-dev",1,0,'k'},
+        {"LRR-smooth-win",1,0,'L'},
         {"AF-file",1,0,'f'},
-        {"baum-welch",1,0,'W'},
+        {"baum-welch",1,0,'W'}, // hidden
+        {"optimize",1,0,'O'},
+        {"aberrant",1,0,'a'},
         {"err-prob",1,0,'e'},
         {"BAF-weight",1,0,'b'},
         {"LRR-weight",1,0,'l'},
@@ -855,9 +1256,52 @@ int main_vcfcnv(int argc, char *argv[])
         {0,0,0,0}
     };
     char *tmp = NULL;
-    while ((c = getopt_long(argc, argv, "h?r:R:t:T:s:o:p:l:T:c:b:P:x:e:W:f:",loptions,NULL)) >= 0) {
+    while ((c = getopt_long(argc, argv, "h?r:R:t:T:s:o:p:l:T:c:b:P:x:e:O:W:f:a:L:d:k:",loptions,NULL)) >= 0) {
         switch (c) {
+            case 'L': 
+                args->lrr_smooth_win = strtol(optarg,&tmp,10);
+                if ( *tmp ) error("Could not parse: --LRR-smooth-win %s\n", optarg);
+                break;
             case 'f': args->af_fname = optarg; break;
+            case 'O': 
+                args->optimize_frac = strtod(optarg,&tmp);
+                if ( *tmp ) error("Could not parse: -O %s\n", optarg);
+                break;
+            case 'd':
+                args->query_sample.baf_dev2_dflt = strtod(optarg,&tmp);
+                if ( *tmp )
+                {
+                    if ( *tmp!=',') error("Could not parse: -d %s\n", optarg);
+                    args->control_sample.baf_dev2_dflt = strtod(tmp+1,&tmp);
+                    if ( *tmp ) error("Could not parse: -d %s\n", optarg);
+                }
+                else
+                    args->control_sample.baf_dev2_dflt = args->query_sample.baf_dev2_dflt;
+                args->query_sample.baf_dev2_dflt   *= args->query_sample.baf_dev2_dflt;
+                args->control_sample.baf_dev2_dflt *= args->control_sample.baf_dev2_dflt;
+                break;
+            case 'k':
+                args->query_sample.lrr_dev2 = strtod(optarg,&tmp);
+                if ( *tmp )
+                {
+                    if ( *tmp!=',') error("Could not parse: -k %s\n", optarg);
+                    args->control_sample.lrr_dev2 = strtod(tmp+1,&tmp);
+                    if ( *tmp ) error("Could not parse: -d %s\n", optarg);
+                }
+                else
+                    args->control_sample.lrr_dev2 = args->query_sample.lrr_dev2;
+                args->query_sample.lrr_dev2   *= args->query_sample.lrr_dev2;
+                args->control_sample.lrr_dev2 *= args->control_sample.lrr_dev2;
+                break;
+            case 'a':
+                args->query_sample.cell_frac_dflt = strtod(optarg,&tmp);
+                if ( *tmp )
+                {
+                    if ( *tmp!=',') error("Could not parse: -a %s\n", optarg);
+                    args->control_sample.cell_frac_dflt = strtod(tmp+1,&tmp);
+                    if ( *tmp ) error("Could not parse: -a %s\n", optarg);
+                }
+                break;
             case 'W':
                 args->baum_welch_th = strtod(optarg,&tmp);
                 if ( *tmp ) error("Could not parse: -W %s\n", optarg);
diff --git a/vcfconcat.c b/vcfconcat.c
index aa46b10..cfec7c0 100644
--- a/vcfconcat.c
+++ b/vcfconcat.c
@@ -1,6 +1,6 @@
 /*  vcfconcat.c -- Concatenate or combine VCF/BCF files.
 
-    Copyright (C) 2013-2014 Genome Research Ltd.
+    Copyright (C) 2013-2015 Genome Research Ltd.
 
     Author: Petr Danecek <pd3 at sanger.ac.uk>
 
@@ -37,7 +37,7 @@ typedef struct _args_t
 {
     bcf_srs_t *files;
     htsFile *out_fh;
-    int output_type;
+    int output_type, n_threads;
     bcf_hdr_t *out_hdr;
     int *seen_seq;
 
@@ -48,8 +48,9 @@ typedef struct _args_t
     int nbuf, mbuf, prev_chr, min_PQ, prev_pos_check;
     int32_t *GTa, *GTb, mGTa, mGTb, *phase_qual, *phase_set;
 
-    char **argv, *output_fname, *file_list, **fnames, *regions_list;
-    int argc, nfnames, allow_overlaps, phased_concat, remove_dups, regions_is_file;
+    char **argv, *output_fname, *file_list, **fnames, *remove_dups, *regions_list;
+    int argc, nfnames, allow_overlaps, phased_concat, regions_is_file;
+    int compact_PS, phase_set_changed;
 }
 args_t;
 
@@ -72,20 +73,15 @@ static void init_data(args_t *args)
     {
         htsFile *fp = hts_open(args->fnames[i], "r"); if ( !fp ) error("Failed to open: %s\n", args->fnames[i]);
         bcf_hdr_t *hdr = bcf_hdr_read(fp); if ( !hdr ) error("Failed to parse header: %s\n", args->fnames[i]);
-        if ( !args->out_hdr )
-            args->out_hdr = bcf_hdr_dup(hdr);
-        else
-        {
-            bcf_hdr_combine(args->out_hdr, hdr);
+        args->out_hdr = bcf_hdr_merge(args->out_hdr,hdr);
+        if ( bcf_hdr_nsamples(hdr) != bcf_hdr_nsamples(args->out_hdr) )
+            error("Different number of samples in %s. Perhaps \"bcftools merge\" is what you are looking for?\n", args->fnames[i]);
 
-            if ( bcf_hdr_nsamples(hdr) != bcf_hdr_nsamples(args->out_hdr) )
-                error("Different number of samples in %s. Perhaps \"bcftools merge\" is what you are looking for?\n", args->fnames[i]);
+        int j;
+        for (j=0; j<bcf_hdr_nsamples(hdr); j++)
+            if ( strcmp(args->out_hdr->samples[j],hdr->samples[j]) )
+                error("Different sample names in %s. Perhaps \"bcftools merge\" is what you are looking for?\n", args->fnames[i]);
 
-            int j;
-            for (j=0; j<bcf_hdr_nsamples(hdr); j++)
-                if ( strcmp(args->out_hdr->samples[j],hdr->samples[j]) )
-                    error("Different sample names in %s. Perhaps \"bcftools merge\" is what you are looking for?\n", args->fnames[i]);
-        }
         if ( args->phased_concat )
         {
             int ret = bcf_read(fp, hdr, line);
@@ -113,6 +109,7 @@ static void init_data(args_t *args)
     bcf_hdr_append_version(args->out_hdr, args->argc, args->argv, "bcftools_concat");
     args->out_fh = hts_open(args->output_fname,hts_bcf_wmode(args->output_type));
     if ( args->out_fh == NULL ) error("Can't write to \"%s\": %s\n", args->output_fname, strerror(errno));
+    if ( args->n_threads ) hts_set_threads(args->out_fh, args->n_threads);
 
     bcf_hdr_write(args->out_fh, args->out_hdr);
 
@@ -125,6 +122,16 @@ static void init_data(args_t *args)
             if ( bcf_sr_set_regions(args->files, args->regions_list, args->regions_is_file)<0 )
                 error("Failed to read the regions: %s\n", args->regions_list);
         }
+        if ( args->remove_dups )
+        {
+            if ( !strcmp(args->remove_dups,"snps") ) args->files->collapse |= COLLAPSE_SNPS;
+            else if ( !strcmp(args->remove_dups,"indels") ) args->files->collapse |= COLLAPSE_INDELS;
+            else if ( !strcmp(args->remove_dups,"both") ) args->files->collapse |= COLLAPSE_SNPS | COLLAPSE_INDELS;
+            else if ( !strcmp(args->remove_dups,"any") ) args->files->collapse |= COLLAPSE_ANY;
+            else if ( !strcmp(args->remove_dups,"all") ) args->files->collapse |= COLLAPSE_ANY;
+            else if ( !strcmp(args->remove_dups,"none") ) args->files->collapse = COLLAPSE_NONE;
+            else error("The -D string \"%s\" not recognised.\n", args->remove_dups);
+        }
         for (i=0; i<args->nfnames; i++)
             if ( !bcf_sr_add_reader(args->files,args->fnames[i]) ) error("Failed to open %s: %s\n", args->fnames[i],bcf_sr_strerror(args->files->errnum));
     }
@@ -190,6 +197,7 @@ int vcf_write_line(htsFile *fp, kstring_t *line);
 static void phase_update(args_t *args, bcf_hdr_t *hdr, bcf1_t *rec)
 {
     int i, nGTs = bcf_get_genotypes(hdr, rec, &args->GTa, &args->mGTa);
+    if ( nGTs <= 0 ) return;    // GT field is not present
     for (i=0; i<bcf_hdr_nsamples(hdr); i++)
     {
         if ( !args->swap_phase[i] ) continue;
@@ -209,6 +217,7 @@ static void phased_flush(args_t *args)
     bcf_hdr_t *bhdr = args->files->readers[1].header;
 
     int i, j, nsmpl = bcf_hdr_nsamples(args->out_hdr);
+    static int gt_absent_warned = 0;
 
     for (i=0; i<args->nbuf; i+=2)
     {
@@ -216,10 +225,26 @@ static void phased_flush(args_t *args)
         bcf1_t *brec = args->buf[i+1];
 
         int nGTs = bcf_get_genotypes(ahdr, arec, &args->GTa, &args->mGTa);
-        if ( nGTs < 0 ) error("GT is not present at %s:%d\n", bcf_seqname(ahdr,arec), arec->pos+1);
+        if ( nGTs < 0 ) 
+        {
+            if ( !gt_absent_warned )
+            {
+                fprintf(stderr,"GT is not present at %s:%d. (This warning is printed only once.)\n", bcf_seqname(ahdr,arec), arec->pos+1);
+                gt_absent_warned = 1;
+            }
+            continue;
+        }
         if ( nGTs != 2*nsmpl ) continue;    // not diploid
         nGTs = bcf_get_genotypes(bhdr, brec, &args->GTb, &args->mGTb);
-        if ( nGTs < 0 ) error("GT is not present at %s:%d\n", bcf_seqname(bhdr,brec), brec->pos+1);
+        if ( nGTs < 0 )
+        {
+            if ( !gt_absent_warned )
+            {
+                fprintf(stderr,"GT is not present at %s:%d. (This warning is printed only once.)\n", bcf_seqname(bhdr,brec), brec->pos+1);
+                gt_absent_warned = 1;
+            }
+            continue;
+        }
         if ( nGTs != 2*nsmpl ) continue;    // not diploid
 
         for (j=0; j<nsmpl; j++)
@@ -246,7 +271,11 @@ static void phased_flush(args_t *args)
         bcf_translate(args->out_hdr, args->files->readers[0].header, arec);
         if ( args->nswap )
             phase_update(args, args->out_hdr, arec);
-        bcf_update_format_int32(args->out_hdr,arec,"PS",args->phase_set,nsmpl);
+        if ( !args->compact_PS || args->phase_set_changed )
+        {
+            bcf_update_format_int32(args->out_hdr,arec,"PS",args->phase_set,nsmpl);
+            args->phase_set_changed = 0;
+        }
         bcf_write(args->out_fh, args->out_hdr, arec);
 
         if ( arec->pos < args->prev_pos_check ) error("FIXME, disorder: %s:%d vs %d  [1]\n", bcf_seqname(args->files->readers[0].header,arec),arec->pos+1,args->prev_pos_check+1);
@@ -283,11 +312,20 @@ static void phased_flush(args_t *args)
             bcf_update_format_int32(args->out_hdr,brec,"PQ",args->phase_qual,nsmpl);
             PQ_printed = 1;
             for (j=0; j<nsmpl; j++)
-                if ( args->phase_qual[j] < args->min_PQ ) args->phase_set[j] = brec->pos+1;
+                if ( args->phase_qual[j] < args->min_PQ ) 
+                {
+                    args->phase_set[j] = brec->pos+1;
+                    args->phase_set_changed = 1;
+                }
+                else if ( args->compact_PS ) args->phase_set[j] = bcf_int32_missing;
         }
         if ( args->nswap )
             phase_update(args, args->out_hdr, brec);
-        bcf_update_format_int32(args->out_hdr,brec,"PS",args->phase_set,nsmpl);
+        if ( !args->compact_PS || args->phase_set_changed )
+        {
+            bcf_update_format_int32(args->out_hdr,brec,"PS",args->phase_set,nsmpl);
+            args->phase_set_changed = 0;
+        }
         bcf_write(args->out_fh, args->out_hdr, brec);
 
         if ( brec->pos < args->prev_pos_check ) error("FIXME, disorder: %s:%d vs %d  [2]\n", bcf_seqname(args->files->readers[1].header,brec),brec->pos+1,args->prev_pos_check+1);
@@ -311,6 +349,7 @@ static void phased_push(args_t *args, bcf1_t *arec, bcf1_t *brec)
 
         for (i=0; i<nsmpl; i++)
             args->phase_set[i] = arec->pos+1;
+        args->phase_set_changed = 1;
 
         if ( args->seen_seq[chr_id] ) error("The chromosome block %s is not contiguous\n", bcf_seqname(args->files->readers[0].header,arec));
         args->seen_seq[chr_id] = 1;
@@ -323,7 +362,11 @@ static void phased_push(args_t *args, bcf1_t *arec, bcf1_t *brec)
         bcf_translate(args->out_hdr, args->files->readers[0].header, arec);
         if ( args->nswap )
             phase_update(args, args->out_hdr, arec);
-        bcf_update_format_int32(args->out_hdr,arec,"PS",args->phase_set,nsmpl);
+        if ( !args->compact_PS || args->phase_set_changed )
+        {
+            bcf_update_format_int32(args->out_hdr,arec,"PS",args->phase_set,nsmpl);
+            args->phase_set_changed = 0;
+        }
         bcf_write(args->out_fh, args->out_hdr, arec);
 
         if ( arec->pos < args->prev_pos_check )
@@ -511,7 +554,7 @@ static void usage(args_t *args)
 {
     fprintf(stderr, "\n");
     fprintf(stderr, "About:   Concatenate or combine VCF/BCF files. All source files must have the same sample\n");
-    fprintf(stderr, "         columns appearing in the same order. Can be used, for example, to\n");
+    fprintf(stderr, "         columns appearing in the same order. The program can be used, for example, to\n");
     fprintf(stderr, "         concatenate chromosome VCFs into one VCF, or combine a SNP VCF and an indel\n");
     fprintf(stderr, "         VCF into one. The input files must be sorted by chr and position. The files\n");
     fprintf(stderr, "         must be given in the correct order to produce sorted VCF on output unless\n");
@@ -520,14 +563,17 @@ static void usage(args_t *args)
     fprintf(stderr, "\n");
     fprintf(stderr, "Options:\n");
     fprintf(stderr, "   -a, --allow-overlaps           First coordinate of the next file can precede last record of the current file.\n");
-    fprintf(stderr, "   -D, --remove-duplicates        Output only once records present in multiple files.\n");
+    fprintf(stderr, "   -c, --compact-PS               Do not output PS tag at each site, only at the start of a new phase set block.\n");
+    fprintf(stderr, "   -d, --rm-dups <string>         Output duplicate records present in multiple files only once: <snps|indels|both|all|none>\n");
+    fprintf(stderr, "   -D, --remove-duplicates        Alias for -d none\n");
     fprintf(stderr, "   -f, --file-list <file>         Read the list of files from a file.\n");
     fprintf(stderr, "   -l, --ligate                   Ligate phased VCFs by matching phase at overlapping haplotypes\n");
-    fprintf(stderr, "   -q, --min-PQ <int>             Break phase set if phasing quality is lower than <int> [30]\n");
     fprintf(stderr, "   -o, --output <file>            Write output to a file [standard output]\n");
     fprintf(stderr, "   -O, --output-type <b|u|z|v>    b: compressed BCF, u: uncompressed BCF, z: compressed VCF, v: uncompressed VCF [v]\n");
-    fprintf(stderr, "   -r, --regions <region>         restrict to comma-separated list of regions\n");
-    fprintf(stderr, "   -R, --regions-file <file>      restrict to regions listed in a file\n");
+    fprintf(stderr, "   -q, --min-PQ <int>             Break phase set if phasing quality is lower than <int> [30]\n");
+    fprintf(stderr, "   -r, --regions <region>         Restrict to comma-separated list of regions\n");
+    fprintf(stderr, "   -R, --regions-file <file>      Restrict to regions listed in a file\n");
+    fprintf(stderr, "       --threads <int>            Number of extra output compression threads [0]\n");
     fprintf(stderr, "\n");
     exit(1);
 }
@@ -539,28 +585,34 @@ int main_vcfconcat(int argc, char *argv[])
     args->argc    = argc; args->argv = argv;
     args->output_fname = "-";
     args->output_type = FT_VCF;
+    args->n_threads = 0;
     args->min_PQ  = 30;
 
     static struct option loptions[] =
     {
-        {"regions",1,0,'r'},
-        {"regions-file",1,0,'R'},
-        {"remove-duplicates",0,0,'D'},
-        {"allow-overlaps",0,0,'a'},
-        {"ligate",0,0,'l'},
-        {"output",1,0,'o'},
-        {"output-type",1,0,'O'},
-        {"file-list",1,0,'f'},
-        {"min-PQ",1,0,'q'},
-        {0,0,0,0}
+        {"compact-PS",no_argument,NULL,'c'},
+        {"regions",required_argument,NULL,'r'},
+        {"regions-file",required_argument,NULL,'R'},
+        {"remove-duplicates",no_argument,NULL,'D'},
+        {"rm-dups",required_argument,NULL,'d'},
+        {"allow-overlaps",no_argument,NULL,'a'},
+        {"ligate",no_argument,NULL,'l'},
+        {"output",required_argument,NULL,'o'},
+        {"output-type",required_argument,NULL,'O'},
+        {"threads",required_argument,NULL,9},
+        {"file-list",required_argument,NULL,'f'},
+        {"min-PQ",required_argument,NULL,'q'},
+        {NULL,0,NULL,0}
     };
     char *tmp;
-    while ((c = getopt_long(argc, argv, "h:?o:O:f:alq:Dr:R:",loptions,NULL)) >= 0)
+    while ((c = getopt_long(argc, argv, "h:?o:O:f:alq:Dd:r:R:c",loptions,NULL)) >= 0)
     {
         switch (c) {
+            case 'c': args->compact_PS = 1; break;
             case 'r': args->regions_list = optarg; break;
             case 'R': args->regions_list = optarg; args->regions_is_file = 1; break;
-            case 'D': args->remove_dups = 1; break;
+            case 'd': args->remove_dups = optarg; break;
+            case 'D': args->remove_dups = "none"; break;
             case 'q': 
                 args->min_PQ = strtol(optarg,&tmp,10);
                 if ( *tmp ) error("Could not parse argument: --min-PQ %s\n", optarg);
@@ -578,6 +630,7 @@ int main_vcfconcat(int argc, char *argv[])
                     default: error("The output type \"%s\" not recognised\n", optarg);
                 };
                 break;
+            case  9 : args->n_threads = strtol(optarg, 0, 0); break;
             case 'h':
             case '?': usage(args); break;
             default: error("Unknown argument: %s\n", optarg);
@@ -591,6 +644,7 @@ int main_vcfconcat(int argc, char *argv[])
         optind++;
     }
     if ( args->allow_overlaps && args->phased_concat ) args->allow_overlaps = 0;
+    if ( args->compact_PS && !args->phased_concat ) error("The -c option is intended only with -l\n");
     if ( args->file_list )
     {
         if ( args->nfnames ) error("Cannot combine -l with file names on command line.\n");
diff --git a/vcfconvert.c b/vcfconvert.c
index 34b12f3..26166df 100644
--- a/vcfconvert.c
+++ b/vcfconvert.c
@@ -66,11 +66,12 @@ struct _args_t
     int nsamples, *samples, sample_is_file, targets_is_file, regions_is_file, output_type;
     char **argv, *sample_list, *targets_list, *regions_list, *tag, *columns;
     char *outfname, *infname, *ref_fname;
-    int argc;
+    int argc, n_threads;
 };
 
 static void destroy_data(args_t *args)
 {
+    if ( args->ref ) fai_destroy(args->ref);
     if ( args->convert) convert_destroy(args->convert);
     if ( args->filter ) filter_destroy(args->filter);
     free(args->samples);
@@ -92,11 +93,12 @@ static void open_vcf(args_t *args, const char *format_str)
     }
     if ( !bcf_sr_add_reader(args->files, args->infname) )
         error("Failed to open %s: %s\n", args->infname,bcf_sr_strerror(args->files->errnum));
-    if ( args->filter_str )
-        args->filter = filter_init(args->header, args->filter_str);
 
     args->header = args->files->readers[0].header;
 
+    if ( args->filter_str )
+        args->filter = filter_init(args->header, args->filter_str);
+
     int i, nsamples = 0, *samples = NULL;
     if ( args->sample_list && strcmp("-",args->sample_list) )
     {
@@ -156,11 +158,19 @@ static int tsv_setter_chrom_pos_ref_alt(tsv_t *tsv, bcf1_t *rec, void *usr)
     if ( *se!='_' ) error("Could not parse REF in CHROM:POS_REF_ALT id: %s\n", tsv->ss);
     kputsn(ss,se-ss,&args->str);
     ss = ++se;
-    while ( se < tsv->se && *se!=':' ) se++;
-    if ( se < tsv->se && *se!=':' ) error("Could not parse ALT in CHROM:POS_REF_ALT id: %s\n", tsv->ss);
+    while ( se < tsv->se && *se!='_' && isspace(*tsv->se) ) se++;
+    if ( se < tsv->se && *se!='_' && isspace(*tsv->se) ) error("Could not parse ALT in CHROM:POS_REF_ALT id: %s\n", tsv->ss);
     kputc(',',&args->str);
     kputsn(ss,se-ss,&args->str);
     bcf_update_alleles_str(args->header, rec, args->str.s);
+
+    // END - optional
+    if (*se && *se=='_') {
+        long end = strtol(se+1,&ss,10);
+        if ( ss==se+1 ) error("Could not parse END in CHROM:POS_REF_ALT_END: %s\n", tsv->ss);
+        bcf_update_info_int32(args->header, rec, "END", &end, 1);
+    }
+
     return 0;
 }
 static int tsv_setter_verify_pos(tsv_t *tsv, bcf1_t *rec, void *usr)
@@ -239,27 +249,61 @@ static int tsv_setter_haps(tsv_t *tsv, bcf1_t *rec, void *usr)
     if ( args->rev_als ) { a0 = bcf_gt_phased(1); a1 = bcf_gt_phased(0); }
     else { a0 = bcf_gt_phased(0); a1 = bcf_gt_phased(1); }
 
+    // up is short for "unphased"
+    int nup = 0; 
     for (i=0; i<nsamples; i++)
     {
-        char *ss = tsv->ss + 4*i;
+        char *ss = tsv->ss + 4*i + nup;
+        int up = 0, all;
+
+        for (all=0; all < 2; all++){
+            // checking for premature ending
+            if ( !ss[0] || !ss[1] || !ss[2] ||
+                 (up && (!ss[3] || !ss[4]) ) )
+            {
+                fprintf(stderr,"Wrong number of fields at %d-th sample ([%c][%c][%c]). ",i+1,ss[0],ss[1],ss[2]);
+                return -1;
+            }
 
-        if ( !ss[0] || !ss[1] || !ss[2] )
+            switch(ss[all*2+up]){
+            case '0':
+                args->gts[2*i+all] = a0;
+                break;
+            case '1' :
+                args->gts[2*i+all] = a1;
+                break;
+            case '?' :
+                // there is no macro to express phased missing allele
+                args->gts[2*i+all] = bcf_gt_phased(-1);
+                break;
+            case '-' :
+                args->gts[2*i+all] = bcf_int32_vector_end;
+                break;
+            default :
+                fprintf(stderr,"Could not parse: [%c][%s]\n", ss[all*2+up],tsv->ss);
+                return -1; 
+            }
+            if( ss[all*2+up+1]=='*' ) up = up + 1;
+        }
+        
+        if(up && up != 2)
         {
-            fprintf(stderr,"Wrong number of fields at %d-th sample ([%c][%c][%c]). ",i+1,ss[0],ss[1],ss[2]);
+            fprintf(stderr,"Missing unphased marker '*': [%c][%s]", ss[2+up], tsv->ss);
             return -1;
         }
 
-        if ( ss[0]=='0' ) args->gts[2*i] = a0;
-        else if ( ss[0]=='1' ) args->gts[2*i] = a1;
-        else { fprintf(stderr,"Could not parse: [%c][%s]\n", ss[0],tsv->ss); return -1; }
-
-        if ( ss[2]=='0' ) args->gts[2*i+1] = a0;
-        else if ( ss[2]=='1' ) args->gts[2*i+1] = a1;
-        else { fprintf(stderr,"Could not parse: [%c][%s]\n", ss[2],tsv->ss); return -1; }
+        // change alleles to unphased if the alleles are unphased
+        if ( up )
+        {
+            args->gts[2*i] = bcf_gt_unphased(bcf_gt_allele(args->gts[2*i]));
+            args->gts[2*i+1] = bcf_gt_unphased(bcf_gt_allele(args->gts[2*i+1]));
+        }
+        nup = nup + up;
     }
-    if ( tsv->ss[(nsamples-1)*4+3] )
+    if ( tsv->ss[(nsamples-1)*4+3+nup] )
     {
-        fprintf(stderr,"Wrong number of fields (%d-th column = [%c]). ", nsamples*2,tsv->ss[(nsamples-1)*4+1]);
+        fprintf(stderr,"nup: %d", nup);
+        fprintf(stderr,"Wrong number of fields (%d-th column = [%c]). ", nsamples*2,tsv->ss[(nsamples-1)*4+nup]);
         return -1;
     }
 
@@ -321,6 +365,7 @@ static void gensample_to_vcf(args_t *args)
     tsv_register(tsv, "GT_GP", tsv_setter_gt_gp, args);
 
     args->header = bcf_hdr_init("w");
+    bcf_hdr_append(args->header, "##INFO=<ID=END,Number=1,Type=Integer,Description=\"End position of the variant described in this record\">");
     bcf_hdr_append(args->header, "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">");
     bcf_hdr_append(args->header, "##FORMAT=<ID=GP,Number=G,Type=Float,Description=\"Genotype Probabilities\">");
     bcf_hdr_printf(args->header, "##contig=<ID=%s,length=%d>", args->str.s,0x7fffffff);   // MAX_CSI_COOR
@@ -338,6 +383,8 @@ static void gensample_to_vcf(args_t *args)
     free(samples);
 
     htsFile *out_fh = hts_open(args->outfname,hts_bcf_wmode(args->output_type));
+    if ( out_fh == NULL ) error("Can't write to \"%s\": %s\n", args->outfname, strerror(errno));
+    if ( args->n_threads ) hts_set_threads(out_fh, args->n_threads);
     bcf_hdr_write(out_fh,args->header);
     bcf1_t *rec = bcf_init();
 
@@ -377,13 +424,14 @@ static void haplegendsample_to_vcf(args_t *args)
      *  Convert from IMPUTE2 hap/legend/sample output files to VCF
      *
      *      hap:
-     *          0 1 0 1 1 1
+     *          0 1 0 1
      *      legend:
      *          id position a0 a1
      *          1:186946386_G_T 186946386 G T
      *      sample:
-     *          QTL190044
-     *          QTL190053
+     *          sample population group sex
+     *          sample1 sample1 sample1 2
+     *          sample2 sample2 sample2 2
      *
      *  Output: VCF with filled GT
      */
@@ -438,23 +486,30 @@ static void haplegendsample_to_vcf(args_t *args)
     tsv_register(hap_tsv, "HAPS", tsv_setter_haps, args);
 
     args->header = bcf_hdr_init("w");
+    bcf_hdr_append(args->header, "##INFO=<ID=END,Number=1,Type=Integer,Description=\"End position of the variant described in this record\">");
     bcf_hdr_append(args->header, "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">");
     bcf_hdr_printf(args->header, "##contig=<ID=%s,length=%d>", args->str.s,0x7fffffff);   // MAX_CSI_COOR
     bcf_hdr_append_version(args->header, args->argc, args->argv, "bcftools_convert");
 
-    int i, nsamples;
-    char **samples = hts_readlist(sample_fname, 1, &nsamples);
-    for (i=0; i<nsamples; i++)
+    int i, nrows, nsamples;
+    char **samples = hts_readlist(sample_fname, 1, &nrows);
+    nsamples = nrows - 1;
+
+    // sample_fname should contain a header line, so need to ignore first row
+    // returned from hts_readlist (i=1, and not i=0)
+    for (i=1; i<nrows; i++)
     {
         se = samples[i]; while ( *se && !isspace(*se) ) se++;
         *se = 0;
         bcf_hdr_add_sample(args->header,samples[i]);
     }
     bcf_hdr_add_sample(args->header,NULL);
-    for (i=0; i<nsamples; i++) free(samples[i]);
+    for (i=0; i<nrows; i++) free(samples[i]);
     free(samples);
 
     htsFile *out_fh = hts_open(args->outfname,hts_bcf_wmode(args->output_type));
+    if ( out_fh == NULL ) error("Can't write to \"%s\": %s\n", args->outfname, strerror(errno));
+    if ( args->n_threads ) hts_set_threads(out_fh, args->n_threads);
     bcf_hdr_write(out_fh,args->header);
     bcf1_t *rec = bcf_init();
 
@@ -548,6 +603,7 @@ static void hapsample_to_vcf(args_t *args)
     tsv_register(tsv, "HAPS", tsv_setter_haps, args);
 
     args->header = bcf_hdr_init("w");
+    bcf_hdr_append(args->header, "##INFO=<ID=END,Number=1,Type=Integer,Description=\"End position of the variant described in this record\">");
     bcf_hdr_append(args->header, "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">");
     bcf_hdr_printf(args->header, "##contig=<ID=%s,length=%d>", args->str.s,0x7fffffff);   // MAX_CSI_COOR
     bcf_hdr_append_version(args->header, args->argc, args->argv, "bcftools_convert");
@@ -565,6 +621,8 @@ static void hapsample_to_vcf(args_t *args)
     free(samples);
 
     htsFile *out_fh = hts_open(args->outfname,hts_bcf_wmode(args->output_type));
+    if ( out_fh == NULL ) error("Can't write to \"%s\": %s\n", args->outfname, strerror(errno));
+    if ( args->n_threads ) hts_set_threads(out_fh, args->n_threads);
     bcf_hdr_write(out_fh,args->header);
     bcf1_t *rec = bcf_init();
 
@@ -677,7 +735,7 @@ static void vcf_to_gensample(args_t *args)
     }
 
     int prev_rid = -1, prev_pos = -1;
-    int no_alt = 0, non_biallelic = 0, filtered = 0, ndup = 0;
+    int no_alt = 0, non_biallelic = 0, filtered = 0, ndup = 0, nok = 0;
     BGZF *gout = bgzf_open(gen_fname, gen_compressed ? "wg" : "wu");
     while ( bcf_sr_next_line(args->files) )
     {
@@ -711,10 +769,11 @@ static void vcf_to_gensample(args_t *args)
         {
             int ret = bgzf_write(gout, str.s, str.l);
             if ( ret!= str.l ) error("Error writing %s: %s\n", gen_fname,strerror(errno));
+            nok++;
         }
     }
-    fprintf(stderr, "%d records skipped: %d/%d/%d/%d no-ALT/non-biallelic/filtered/duplicated\n", 
-        no_alt+non_biallelic+filtered+ndup, no_alt, non_biallelic, filtered, ndup);
+    fprintf(stderr, "%d records written, %d skipped: %d/%d/%d/%d no-ALT/non-biallelic/filtered/duplicated\n", 
+        nok, no_alt+non_biallelic+filtered+ndup, no_alt, non_biallelic, filtered, ndup);
 
     if ( str.m ) free(str.s);
     if ( bgzf_close(gout)!=0 ) error("Error closing %s: %s\n", gen_fname,strerror(errno));
@@ -802,7 +861,7 @@ static void vcf_to_haplegendsample(args_t *args)
         if ( ret != str.l ) error("Error writing %s: %s\n", legend_fname, strerror(errno));
     }
 
-    int no_alt = 0, non_biallelic = 0, filtered = 0;
+    int no_alt = 0, non_biallelic = 0, filtered = 0, nok = 0;
     while ( bcf_sr_next_line(args->files) )
     {
         bcf1_t *line = bcf_sr_get_line(args->files,0);
@@ -843,8 +902,9 @@ static void vcf_to_haplegendsample(args_t *args)
             ret = bgzf_write(lout, str.s, str.l);
             if ( ret != str.l ) error("Error writing %s: %s\n", legend_fname, strerror(errno));
         }
+        nok++;
     }
-    fprintf(stderr, "%d records skipped: %d/%d/%d no-ALT/non-biallelic/filtered\n", no_alt+non_biallelic+filtered, no_alt, non_biallelic, filtered);
+    fprintf(stderr, "%d records written, %d skipped: %d/%d/%d no-ALT/non-biallelic/filtered\n", nok,no_alt+non_biallelic+filtered, no_alt, non_biallelic, filtered);
     if ( str.m ) free(str.s);
     if ( hout && bgzf_close(hout)!=0 ) error("Error closing %s: %s\n", hap_fname, strerror(errno));
     if ( lout && bgzf_close(lout)!=0 ) error("Error closing %s: %s\n", legend_fname, strerror(errno));
@@ -935,7 +995,7 @@ static void vcf_to_hapsample(args_t *args)
     // open haps output
     BGZF *hout = hap_fname ? bgzf_open(hap_fname, hap_compressed ? "wg" : "wu") : NULL;
 
-    int no_alt = 0, non_biallelic = 0, filtered = 0;
+    int no_alt = 0, non_biallelic = 0, filtered = 0, nok = 0;
     while ( bcf_sr_next_line(args->files) )
     {
         bcf1_t *line = bcf_sr_get_line(args->files,0);
@@ -965,8 +1025,9 @@ static void vcf_to_hapsample(args_t *args)
             ret = bgzf_write(hout, str.s, str.l); // write hap file
             if ( ret != str.l ) error("Error writing %s: %s\n", hap_fname, strerror(errno));
         }
+        nok++;
     }
-    fprintf(stderr, "%d records skipped: %d/%d/%d no-ALT/non-biallelic/filtered\n", no_alt+non_biallelic+filtered, no_alt, non_biallelic, filtered);
+    fprintf(stderr, "%d records written, %d skipped: %d/%d/%d no-ALT/non-biallelic/filtered\n", nok, no_alt+non_biallelic+filtered, no_alt, non_biallelic, filtered);
     if ( str.m ) free(str.s);
     if ( hout && bgzf_close(hout)!=0 ) error("Error closing %s: %s\n", hap_fname, strerror(errno));
     if (hap_fname) free(hap_fname);
@@ -1073,8 +1134,8 @@ static int tsv_setter_aa(tsv_t *tsv, bcf1_t *rec, void *usr)
 
 static void tsv_to_vcf(args_t *args)
 {
-    if ( !args->ref_fname ) error("Missing the --ref option\n");
-    if ( !args->sample_list ) error("Missing the --samples option\n");
+    if ( !args->ref_fname ) error("--tsv2vcf requires the --fasta-ref option\n");
+    if ( !args->sample_list ) error("--tsv2vcf requires the --samples option\n");
 
     args->ref = fai_load(args->ref_fname);
     if ( !args->ref ) error("Could not load the reference %s\n", args->ref_fname);
@@ -1097,6 +1158,8 @@ static void tsv_to_vcf(args_t *args)
     args->gts = (int32_t *) malloc(sizeof(int32_t)*n*2);
 
     htsFile *out_fh = hts_open(args->outfname,hts_bcf_wmode(args->output_type));
+    if ( out_fh == NULL ) error("Can't write to \"%s\": %s\n", args->outfname, strerror(errno));
+    if ( args->n_threads ) hts_set_threads(out_fh, args->n_threads);
     bcf_hdr_write(out_fh,args->header);
 
     tsv_t *tsv = tsv_init(args->columns ? args->columns : "ID,CHROM,POS,AA");
@@ -1125,7 +1188,6 @@ static void tsv_to_vcf(args_t *args)
     if ( hts_close(in_fh) ) error("Close failed: %s\n", args->infname);
     free(line.s);
 
-    fai_destroy(args->ref);
     bcf_hdr_destroy(args->header);
     hts_close(out_fh);
     tsv_destroy(tsv);
@@ -1146,7 +1208,8 @@ static void vcf_to_vcf(args_t *args)
 {
     open_vcf(args,NULL);
     htsFile *out_fh = hts_open(args->outfname,hts_bcf_wmode(args->output_type));
-    if ( !out_fh ) error("Failed to open: %s\n", args->outfname);
+    if ( out_fh == NULL ) error("Can't write to \"%s\": %s\n", args->outfname, strerror(errno));
+    if ( args->n_threads ) hts_set_threads(out_fh, args->n_threads);
 
     bcf_hdr_t *hdr = bcf_sr_get_header(args->files,0);
     bcf_hdr_write(out_fh,hdr);
@@ -1167,9 +1230,15 @@ static void vcf_to_vcf(args_t *args)
 
 static void gvcf_to_vcf(args_t *args)
 {
+    if ( !args->ref_fname ) error("--gvcf2vcf requires the --fasta-ref option\n");
+
+    args->ref = fai_load(args->ref_fname);
+    if ( !args->ref ) error("Could not load the fai index for reference %s\n", args->ref_fname);
+
     open_vcf(args,NULL);
     htsFile *out_fh = hts_open(args->outfname,hts_bcf_wmode(args->output_type));
-    if ( !out_fh ) error("Failed to open: %s\n", args->outfname);
+    if ( out_fh == NULL ) error("Can't write to \"%s\": %s\n", args->outfname, strerror(errno));
+    if ( args->n_threads ) hts_set_threads(out_fh, args->n_threads);
 
     bcf_hdr_t *hdr = bcf_sr_get_header(args->files,0);
     bcf_hdr_append_version(hdr, args->argc, args->argv, "bcftools_convert");
@@ -1202,10 +1271,15 @@ static void gvcf_to_vcf(args_t *args)
             continue;
         }
         bcf_update_info_int32(hdr,line,"END",NULL,0);
-        int pos;
-        for (pos=line->pos; pos<=itmp[0]; pos++)
+        int pos, len;
+        for (pos=line->pos; pos<itmp[0]; pos++)
         {
             line->pos = pos;
+            char *ref = faidx_fetch_seq(args->ref, (char*)bcf_hdr_id2name(hdr,line->rid), line->pos, line->pos, &len);
+            if ( !ref ) error("faidx_fetch_seq failed at %s:%d\n", bcf_hdr_id2name(hdr,line->rid), line->pos+1);
+            // we have already checked above that there is only one allele,
+            // so fine to just update alleles with the ref allele from the fasta
+            bcf_update_alleles_str(hdr, line, &ref[0]);
             bcf_write(out_fh,hdr,line);
         }
     }
@@ -1230,6 +1304,7 @@ static void usage(void)
     fprintf(stderr, "   -S, --samples-file <file>   file of samples to include\n");
     fprintf(stderr, "   -t, --targets <region>      similar to -r but streams rather than index-jumps\n");
     fprintf(stderr, "   -T, --targets-file <file>   similar to -R but streams rather than index-jumps\n");
+    fprintf(stderr, "       --threads <int>         number of extra output compression threads [0]\n");
     fprintf(stderr, "\n");
     fprintf(stderr, "VCF output options:\n");
     fprintf(stderr, "   -o, --output <file>            output file name [stdout]\n");
@@ -1243,7 +1318,8 @@ static void usage(void)
     fprintf(stderr, "       --vcf-ids               output VCF IDs in second column instead of CHROM:POS_REF_ALT\n");
     fprintf(stderr, "\n");
     fprintf(stderr, "gVCF conversion:\n");
-    fprintf(stderr, "       --gvcf2vcf              \n");
+    fprintf(stderr, "       --gvcf2vcf              expand gVCF reference blocks\n");
+    fprintf(stderr, "   -f, --fasta-ref <file>      reference sequence in fasta format\n");
     fprintf(stderr, "\n");
     fprintf(stderr, "HAP/SAMPLE conversion (output from SHAPEIT):\n");
     fprintf(stderr, "       --hapsample2vcf <...>   <prefix>|<haps-file>,<sample-file>\n");
@@ -1282,6 +1358,7 @@ int main_vcfconvert(int argc, char *argv[])
     args->argc   = argc; args->argv = argv;
     args->outfname = "-";
     args->output_type = FT_VCF;
+    args->n_threads = 0;
 
     static struct option loptions[] =
     {
@@ -1289,6 +1366,7 @@ int main_vcfconvert(int argc, char *argv[])
         {"exclude",required_argument,NULL,'e'},
         {"output",required_argument,NULL,'o'},
         {"output-type",required_argument,NULL,'O'},
+        {"threads",required_argument,NULL,9},
         {"regions",required_argument,NULL,'r'},
         {"regions-file",required_argument,NULL,'R'},
         {"targets",required_argument,NULL,'t'},
@@ -1309,7 +1387,7 @@ int main_vcfconvert(int argc, char *argv[])
         {"haplegendsample2vcf",required_argument,NULL,'H'},
         {"columns",required_argument,NULL,'c'},
         {"fasta-ref",required_argument,NULL,'f'},
-        {0,0,0,0}
+        {NULL,0,NULL,0}
     };
     while ((c = getopt_long(argc, argv, "?h:r:R:s:S:t:T:i:e:g:G:o:O:c:f:H:",loptions,NULL)) >= 0) {
         switch (c) {
@@ -1345,6 +1423,7 @@ int main_vcfconvert(int argc, char *argv[])
                 }
                 break;
             case 'h': args->convert_func = vcf_to_haplegendsample; args->outfname = optarg; break;
+            case  9 : args->n_threads = strtol(optarg, 0, 0); break;
             case '?': usage();
             default: error("Unknown argument: %s\n", optarg);
         }
diff --git a/vcffilter.c b/vcffilter.c
index 481941c..ac4c3a3 100644
--- a/vcffilter.c
+++ b/vcffilter.c
@@ -68,7 +68,7 @@ typedef struct _args_t
     bcf_srs_t *files;
     bcf_hdr_t *hdr;
     htsFile *out_fh;
-    int output_type;
+    int output_type, n_threads;
 
     char **argv, *output_fname, *targets_list, *regions_list;
     int argc;
@@ -79,6 +79,7 @@ static void init_data(args_t *args)
 {
     args->out_fh = hts_open(args->output_fname,hts_bcf_wmode(args->output_type));
     if ( args->out_fh == NULL ) error("Can't write to \"%s\": %s\n", args->output_fname, strerror(errno));
+    if ( args->n_threads ) hts_set_threads(args->out_fh, args->n_threads);
 
     args->hdr = args->files->readers[0].header;
     args->flt_pass = bcf_hdr_id2int(args->hdr,BCF_DT_ID,"PASS"); assert( !args->flt_pass );  // sanity check: required by BCF spec
@@ -227,7 +228,7 @@ static void buffered_filters(args_t *args, bcf1_t *line)
         if ( ilast>=0 && line->rid != args->rbuf_lines[ilast]->rid )
             flush_buffer(args, args->rbuf.n); // new chromosome, flush everything
 
-        if ( args->rbuf.n >= args->rbuf.m ) rbuf_expand0(&args->rbuf,bcf1_t*,args->rbuf_lines);
+        rbuf_expand0(&args->rbuf,bcf1_t*,args->rbuf.n,args->rbuf_lines);
 
         // Insert the new record in the buffer. The line would be overwritten in
         // the next bcf_sr_next_line call, therefore we need to swap it with an
@@ -415,6 +416,7 @@ static void usage(args_t *args)
     fprintf(stderr, "    -S, --set-GTs <.|0>           set genotypes of failed samples to missing (.) or ref (0)\n");
     fprintf(stderr, "    -t, --targets <region>        similar to -r but streams rather than index-jumps\n");
     fprintf(stderr, "    -T, --targets-file <file>     similar to -R but streams rather than index-jumps\n");
+    fprintf(stderr, "        --threads <int>           number of extra output compression threads [0]\n");
     fprintf(stderr, "\n");
     exit(1);
 }
@@ -427,24 +429,26 @@ int main_vcffilter(int argc, char *argv[])
     args->files   = bcf_sr_init();
     args->output_fname = "-";
     args->output_type = FT_VCF;
+    args->n_threads = 0;
     int regions_is_file = 0, targets_is_file = 0;
 
     static struct option loptions[] =
     {
-        {"set-GTs",1,0,'S'},
-        {"mode",1,0,'m'},
-        {"soft-filter",1,0,'s'},
-        {"exclude",1,0,'e'},
-        {"include",1,0,'i'},
-        {"targets",1,0,'t'},
-        {"targets-file",1,0,'T'},
-        {"regions",1,0,'r'},
-        {"regions-file",1,0,'R'},
-        {"output",1,0,'o'},
-        {"output-type",1,0,'O'},
-        {"SnpGap",1,0,'g'},
-        {"IndelGap",1,0,'G'},
-        {0,0,0,0}
+        {"set-GTs",required_argument,NULL,'S'},
+        {"mode",required_argument,NULL,'m'},
+        {"soft-filter",required_argument,NULL,'s'},
+        {"exclude",required_argument,NULL,'e'},
+        {"include",required_argument,NULL,'i'},
+        {"targets",required_argument,NULL,'t'},
+        {"targets-file",required_argument,NULL,'T'},
+        {"regions",required_argument,NULL,'r'},
+        {"regions-file",required_argument,NULL,'R'},
+        {"output",required_argument,NULL,'o'},
+        {"output-type",required_argument,NULL,'O'},
+        {"threads",required_argument,NULL,9},
+        {"SnpGap",required_argument,NULL,'g'},
+        {"IndelGap",required_argument,NULL,'G'},
+        {NULL,0,NULL,0}
     };
     char *tmp;
     while ((c = getopt_long(argc, argv, "e:i:t:T:r:R:h?s:m:o:O:g:G:S:",loptions,NULL)) >= 0) {
@@ -483,6 +487,7 @@ int main_vcffilter(int argc, char *argv[])
                 else if ( !strcmp("0",optarg) ) args->set_gts = SET_GTS_REF;
                 else error("The argument to -S not recognised: %s\n", optarg);
                 break;
+            case  9 : args->n_threads = strtol(optarg, 0, 0); break;
             case 'h':
             case '?': usage(args);
             default: error("Unknown argument: %s\n", optarg);
diff --git a/vcfgtcheck.c b/vcfgtcheck.c
index e3f03cc..b741ef6 100644
--- a/vcfgtcheck.c
+++ b/vcfgtcheck.c
@@ -88,7 +88,7 @@ static void plot_check(args_t *args, char *target_sample, char *query_sample)
             "        if row[4]=='%s': tgt = 1\n"
             "        dat.append([float(row[1]), float(row[2]), float(row[3]), tgt, row[4]])\n"
             "\n"
-            "dat = sorted(dat, reverse=True)\n"
+            "dat = sorted(dat)\n"
             "\n"
             "iq = -1; dp = 0\n"
             "for i in range(len(dat)):\n"
@@ -99,7 +99,7 @@ static void plot_check(args_t *args, char *target_sample, char *query_sample)
             "fig,ax1 = plt.subplots(figsize=(8,5))\n"
             "ax2 = ax1.twinx()\n"
             "plots  = ax1.plot([x[0] for x in dat],'o-', ms=3, color='g', mec='g', label='Discordance (total)')\n"
-            "plots += ax1.plot([x[1] for x in dat], '^', ms=3, color='r', mec='r', label='Discordance (per site)')\n"
+            "plots += ax1.plot([x[1] for x in dat], '^', ms=3, color='r', mec='r', label='Discordance (avg per site)')\n"
             "plots += ax2.plot([x[2] for x in dat],'v', ms=3, color='k', label='Number of sites')\n"
             "if iq!=-1:\n"
             "   ax1.plot([iq],[dat[iq][0]],'o',color='orange', ms=9)\n"
@@ -107,6 +107,9 @@ static void plot_check(args_t *args, char *target_sample, char *query_sample)
             "   ax1.plot([iq],[dat[iq][1]],'^',color='red', ms=5)\n"
             "for tl in ax1.get_yticklabels(): tl.set_color('g')\n"
             "for tl in ax2.get_yticklabels(): tl.set_color('k'); tl.set_fontsize(9)\n"
+            "min_dp = min([x[2] for x in dat])\n"
+            "max_dp = max([x[2] for x in dat])\n"
+            "ax2.set_ylim(min_dp-1,max_dp+1)\n"
             "ax1.set_title('Discordance with %s')\n"
             "ax1.set_xlim(-0.05*len(dat),1.05*(len(dat)-1))\n"
             "ax1.set_xlabel('Sample ID')\n"
@@ -408,8 +411,18 @@ static void check_gt(args_t *args)
         if ( !fake_pls )
         {
             if ( (npl=bcf_get_format_int32(args->sm_hdr, sm_line, "PL", &args->pl_arr, &args->npl_arr)) <= 0 )
-                error("PL not present at %s:%d?", args->sm_hdr->id[BCF_DT_CTG][sm_line->rid].key, sm_line->pos+1);
-            npl /= bcf_hdr_nsamples(args->sm_hdr);
+            {
+                if ( sm_line->n_allele==1 )
+                {
+                    // PL values may not be present when ALT=. (mpileup/bcftools output), in that case 
+                    // switch automatically to GT at these sites
+                    npl = fake_PLs(args, args->sm_hdr, sm_line);
+                }
+                else
+                    error("PL not present at %s:%d?\n", args->sm_hdr->id[BCF_DT_CTG][sm_line->rid].key, sm_line->pos+1);
+            }
+            else
+                npl /= bcf_hdr_nsamples(args->sm_hdr);
         }
         else
             npl = fake_PLs(args, args->sm_hdr, sm_line);
@@ -486,7 +499,7 @@ static void check_gt(args_t *args)
     for (i=0; i<nsamples; i++) p[i] = &args->lks[i];
     qsort(p, nsamples, sizeof(int*), cmp_doubleptr);
 
-    fprintf(fp, "# [1]CN\t[2]Discordance with %s (total)\t[3]Discordance (score per site)\t[4]Number of sites compared\t[5]Sample\t[6]Sample ID\n", args->sm_hdr->samples[query_isample]);
+    fprintf(fp, "# [1]CN\t[2]Discordance with %s (total)\t[3]Discordance (avg score per site)\t[4]Number of sites compared\t[5]Sample\t[6]Sample ID\n", args->sm_hdr->samples[query_isample]);
     for (i=0; i<nsamples; i++)
     {
         int idx = p[i] - args->lks;
@@ -564,7 +577,8 @@ static void cross_check_gts(args_t *args)
         }
         else
             npl = fake_PLs(args, args->sm_hdr, line);
-        if ( !ignore_dp && bcf_get_format_int32(args->sm_hdr, line, "DP", &dp_arr, &ndp_arr) <= 0 ) { dp_warned++; continue; }
+        int mdp = 0;
+        if ( !ignore_dp && (mdp=bcf_get_format_int32(args->sm_hdr, line, "DP", &dp_arr, &ndp_arr)) <= 0 ) dp_warned++;
 
         if ( args->hom_only )
         {
@@ -578,14 +592,14 @@ static void cross_check_gts(args_t *args)
         {
             int *ipl = &args->pl_arr[i*npl];
             if ( *ipl==-1 ) { idx += i; continue; } // missing genotype
-            if ( !ignore_dp && (dp_arr[i]==bcf_int32_missing || !dp_arr[i]) ) { idx += i; continue; }
+            if ( mdp>0 && (dp_arr[i]==bcf_int32_missing || !dp_arr[i]) ) { idx += i; continue; }
             if ( args->hom_only && !is_hom[i] ) { idx += i; continue; }
 
             for (j=0; j<i; j++)
             {
                 int *jpl = &args->pl_arr[j*npl];
                 if ( *jpl==-1 ) { idx++; continue; } // missing genotype
-                if ( !ignore_dp && (dp_arr[j]==bcf_int32_missing || !dp_arr[j]) ) { idx++; continue; }
+                if ( mdp>0 && (dp_arr[j]==bcf_int32_missing || !dp_arr[j]) ) { idx++; continue; }
                 if ( args->hom_only && !is_hom[j] ) { idx++; continue; }
 
                 int min_pl = INT_MAX;
@@ -601,7 +615,7 @@ static void cross_check_gts(args_t *args)
                 args->lks[idx] += min_pl;
                 args->cnts[idx]++;
 
-                if ( !ignore_dp )
+                if ( mdp>0 )
                 {
                     args->dps[idx] += dp_arr[i] < dp_arr[j] ? dp_arr[i] : dp_arr[j];
                     dp[i] += dp_arr[i]; ndp[i]++;
diff --git a/vcfindex.c b/vcfindex.c
index 24ac8a8..e40fab5 100644
--- a/vcfindex.c
+++ b/vcfindex.c
@@ -97,13 +97,7 @@ int vcf_index_stats(char *fname, int stats)
         if (stats&2 || !records) continue;
         bcf_hrec_t *hrec = bcf_hdr_get_hrec(hdr, BCF_HL_CTG, "ID", seq[i], NULL);
         int hkey = hrec ? bcf_hrec_find_key(hrec, "length") : -1;
-        if (hkey<0)
-        {
-            fprintf(stderr,"could not get contig length for %s\n", seq[i]);
-            return 1;
-        }
-        fprintf(out, "%s\t%s", seq[i], strcmp(hrec->vals[hkey], "2147483647")==0 ? "." : hrec->vals[hkey]);
-        fprintf(out, "\t%" PRIu64 "\n", records);
+        fprintf(out,"%s\t%s\t%" PRIu64 "\n", seq[i], hkey<0?".":hrec->vals[hkey], records);
     }
     if (!sum)
     {
diff --git a/vcfisec.c b/vcfisec.c
index 27b8129..6115146 100644
--- a/vcfisec.c
+++ b/vcfisec.c
@@ -41,6 +41,7 @@ THE SOFTWARE.  */
 #define OP_EQUAL 3
 #define OP_VENN 4
 #define OP_COMPLEMENT 5
+#define OP_EXACT 6
 
 // Logic of the filters: include or exclude sites which match the filters?
 #define FLT_INCLUDE 1
@@ -48,7 +49,7 @@ THE SOFTWARE.  */
 
 typedef struct
 {
-    int isec_op, isec_n, *write, iwrite, nwrite, output_type;
+    int isec_op, isec_n, *write, iwrite, nwrite, output_type, n_threads;
     int nflt, *flt_logic;
     filter_t **flt;
     char **flt_expr;
@@ -56,6 +57,7 @@ typedef struct
     FILE *fh_log, *fh_sites;
     htsFile **fh_out;
     char **argv, *prefix, *output_fname, **fnames, *write_files, *targets_list, *regions_list;
+    char *isec_exact;
     int argc;
 }
 args_t;
@@ -126,14 +128,6 @@ FILE *open_file(char **fname, const char *mode, const char *fmt, ...)
     return fp;
 }
 
-const char *hts_bcf_wmode(int file_type)
-{
-    if ( file_type == FT_BCF ) return "wbu";    // uncompressed BCF
-    if ( file_type & FT_BCF ) return "wb";      // compressed BCF
-    if ( file_type & FT_GZ ) return "wz";       // compressed VCF
-    return "w";                                 // uncompressed VCF
-}
-
 void isec_vcf(args_t *args)
 {
     bcf_srs_t *files = args->files;
@@ -148,6 +142,7 @@ void isec_vcf(args_t *args)
     {
         out_fh = hts_open(args->output_fname? args->output_fname : "-",hts_bcf_wmode(args->output_type));
         if ( out_fh == NULL ) error("Can't write to %s: %s\n", args->output_fname? args->output_fname : "standard output", strerror(errno));
+        if ( args->n_threads ) hts_set_threads(out_fh, args->n_threads);
         bcf_hdr_append_version(files->readers[args->iwrite].header,args->argc,args->argv,"bcftools_isec");
         bcf_hdr_write(out_fh, files->readers[args->iwrite].header);
     }
@@ -190,7 +185,12 @@ void isec_vcf(args_t *args)
             case OP_COMPLEMENT: if ( n!=1 || !bcf_sr_has_line(files,0) ) continue; break;
             case OP_EQUAL: if ( n != args->isec_n ) continue; break;
             case OP_PLUS: if ( n < args->isec_n ) continue; break;
-            case OP_MINUS: if ( n > args->isec_n ) continue;
+            case OP_MINUS: if ( n > args->isec_n ) continue; break;
+            case OP_EXACT:
+                for (i=0; i<files->nreaders; i++)
+                    if ( files->has_line[i] != args->isec_exact[i] ) break;
+                if ( i<files->nreaders ) continue;
+                break;
         }
 
         if ( out_std )
@@ -294,6 +294,16 @@ static void init_data(args_t *args)
         }
     }
 
+    if ( args->isec_op==OP_EXACT )
+    {
+        if ( strlen(args->isec_exact)!=args->files->nreaders )
+            error("The number of files does not match the bitmask: %d vs %s\n", args->files->nreaders,args->isec_exact);
+        for (i=0; i<args->files->nreaders; i++)
+            if ( args->isec_exact[i]!='0' && args->isec_exact[i]!='1' ) error("Unexpected bitmask: %s\n",args->isec_exact);
+        for (i=0; i<args->files->nreaders; i++)
+            args->isec_exact[i] -= '0';
+    }
+
     // Which files to write: parse the string passed with -w
     char *p = args->write_files;
     while (p && *p)
@@ -340,6 +350,7 @@ static void init_data(args_t *args)
                 open_file(&args->fnames[i], NULL, "%s/%04d.%s", args->prefix, i, suffix); \
                 args->fh_out[i] = hts_open(args->fnames[i], hts_bcf_wmode(args->output_type));  \
                 if ( !args->fh_out[i] ) error("Could not open %s\n", args->fnames[i]); \
+                if ( args->n_threads ) hts_set_threads(args->fh_out[i], args->n_threads); \
                 bcf_hdr_append_version(args->files->readers[j].header,args->argc,args->argv,"bcftools_isec"); \
                 bcf_hdr_write(args->fh_out[i], args->files->readers[j].header); \
             }
@@ -445,7 +456,7 @@ static void usage(void)
     fprintf(stderr, "    -e, --exclude <expr>          exclude sites for which the expression is true\n");
     fprintf(stderr, "    -f, --apply-filters <list>    require at least one of the listed FILTER strings (e.g. \"PASS,.\")\n");
     fprintf(stderr, "    -i, --include <expr>          include only sites for which the expression is true\n");
-    fprintf(stderr, "    -n, --nfiles [+-=]<int>       output positions present in this many (=), this many or more (+), or this many or fewer (-) files\n");
+    fprintf(stderr, "    -n, --nfiles [+-=~]<int>      output positions present in this many (=), this many or more (+), this many or fewer (-), the exact (~) files\n");
     fprintf(stderr, "    -o, --output <file>           write output to a file [standard output]\n");
     fprintf(stderr, "    -O, --output-type <b|u|z|v>   b: compressed BCF, u: uncompressed BCF, z: compressed VCF, v: uncompressed VCF [v]\n");
     fprintf(stderr, "    -p, --prefix <dir>            if given, subset each of the input files accordingly, see also -w\n");
@@ -454,6 +465,7 @@ static void usage(void)
     fprintf(stderr, "    -t, --targets <region>        similar to -r but streams rather than index-jumps\n");
     fprintf(stderr, "    -T, --targets-file <file>     similar to -R but streams rather than index-jumps\n");
     fprintf(stderr, "    -w, --write <list>            list of files to write with -p given as 1-based indexes. By default, all files are written\n");
+    fprintf(stderr, "        --threads <int>           number of extra output compression threads [0]\n");
     fprintf(stderr, "\n");
     fprintf(stderr, "Examples:\n");
     fprintf(stderr, "   # Create intersection and complements of two sets saving the output in dir/*\n");
@@ -479,26 +491,28 @@ int main_vcfisec(int argc, char *argv[])
     args->argc   = argc; args->argv = argv;
     args->output_fname = NULL;
     args->output_type = FT_VCF;
+    args->n_threads = 0;
     int targets_is_file = 0, regions_is_file = 0;
 
     static struct option loptions[] =
     {
-        {"help",0,0,'h'},
-        {"exclude",1,0,'e'},
-        {"include",1,0,'i'},
-        {"collapse",1,0,'c'},
-        {"complement",0,0,'C'},
-        {"apply-filters",1,0,'f'},
-        {"nfiles",1,0,'n'},
-        {"prefix",1,0,'p'},
-        {"write",1,0,'w'},
-        {"targets",1,0,'t'},
-        {"targets-file",1,0,'T'},
-        {"regions",1,0,'r'},
-        {"regions-file",1,0,'R'},
-        {"output",1,0,'o'},
-        {"output-type",1,0,'O'},
-        {0,0,0,0}
+        {"help",no_argument,NULL,'h'},
+        {"exclude",required_argument,NULL,'e'},
+        {"include",required_argument,NULL,'i'},
+        {"collapse",required_argument,NULL,'c'},
+        {"complement",no_argument,NULL,'C'},
+        {"apply-filters",required_argument,NULL,'f'},
+        {"nfiles",required_argument,NULL,'n'},
+        {"prefix",required_argument,NULL,'p'},
+        {"write",required_argument,NULL,'w'},
+        {"targets",required_argument,NULL,'t'},
+        {"targets-file",required_argument,NULL,'T'},
+        {"regions",required_argument,NULL,'r'},
+        {"regions-file",required_argument,NULL,'R'},
+        {"output",required_argument,NULL,'o'},
+        {"output-type",required_argument,NULL,'O'},
+        {"threads",required_argument,NULL,9},
+        {NULL,0,NULL,0}
     };
     while ((c = getopt_long(argc, argv, "hc:r:R:p:n:w:t:T:Cf:o:O:i:e:",loptions,NULL)) >= 0) {
         switch (c) {
@@ -538,11 +552,14 @@ int main_vcfisec(int argc, char *argv[])
                     if ( *p=='-' ) { args->isec_op = OP_MINUS; p++; }
                     else if ( *p=='+' ) { args->isec_op = OP_PLUS; p++; }
                     else if ( *p=='=' ) { args->isec_op = OP_EQUAL; p++; }
+                    else if ( *p=='~' ) { args->isec_op = OP_EXACT; p++; }
                     else if ( isdigit(*p) ) args->isec_op = OP_EQUAL;
                     else error("Could not parse --nfiles %s\n", optarg);
-                    if ( sscanf(p,"%d",&args->isec_n)!=1 ) error("Could not parse --nfiles %s\n", optarg);
+                    if ( args->isec_op == OP_EXACT ) args->isec_exact = p;
+                    else if ( sscanf(p,"%d",&args->isec_n)!=1 ) error("Could not parse --nfiles %s\n", optarg);
                 }
                 break;
+            case  9 : args->n_threads = strtol(optarg, 0, 0); break;
             case 'h':
             case '?': usage();
             default: error("Unknown argument: %s\n", optarg);
diff --git a/vcfmerge.c b/vcfmerge.c
index ea26903..0517bd5 100644
--- a/vcfmerge.c
+++ b/vcfmerge.c
@@ -118,7 +118,7 @@ typedef struct
     htsFile *out_fh;
     bcf_hdr_t *out_hdr;
     char **argv;
-    int argc;
+    int argc, n_threads;
 }
 args_t;
 
@@ -421,11 +421,10 @@ static int info_rules_add_values(args_t *args, bcf_hdr_t *hdr, bcf1_t *line, inf
 
 int bcf_hdr_sync(bcf_hdr_t *h);
 
-void bcf_hdr_merge(bcf_hdr_t *hw, const bcf_hdr_t *hr, const char *clash_prefix, int force_samples)
+void merge_headers(bcf_hdr_t *hw, const bcf_hdr_t *hr, const char *clash_prefix, int force_samples)
 {
     // header lines
-    int ret = bcf_hdr_combine(hw, hr);
-    if ( ret!=0 ) error("Error occurred while merging the headers.\n");
+    hw = bcf_hdr_merge(hw, hr);
 
     // samples
     int i;
@@ -578,7 +577,7 @@ char **merge_alleles(char **a, int na, int *map, char **b, int *nb, int *mb)
             ai = a[i];
 
         for (j=1; j<*nb; j++)
-            if ( !strcmp(ai,b[j]) ) break;
+            if ( !strcasecmp(ai,b[j]) ) break;
 
         if ( j<*nb ) // $b already has the same allele
         {
@@ -789,7 +788,7 @@ void merge_filter(args_t *args, bcf1_t *out)
             if ( kitr == kh_end(tmph) )
             {
                 int id = bcf_hdr_id2int(out_hdr, BCF_DT_ID, flt);
-                if ( id==-1 ) error("The filter not defined: %s\n", flt);
+                if ( id==-1 ) error("Error: The filter is not defined in the header: %s\n", flt);
                 hts_expand(int,out->d.n_flt+1,ma->mflt,ma->flt);
                 ma->flt[out->d.n_flt] = id;
                 out->d.n_flt++;
@@ -1775,7 +1774,7 @@ void merge_buffer(args_t *args)
 
             // normalize alleles
             maux->als = merge_alleles(line->d.allele, line->n_allele, maux->d[i][j].map, maux->als, &maux->nals, &maux->mals);
-            if ( !maux->als ) error("Failed to merge alleles at %s:%d in %s\n",bcf_seqname(args->out_hdr,line),line->pos+1,reader->fname);
+            if ( !maux->als ) error("Failed to merge alleles at %s:%d in %s\n",bcf_seqname(bcf_sr_get_header(args->files,j),line),line->pos+1,reader->fname);
             hts_expand0(int, maux->nals, maux->ncnt, maux->cnt);
             for (k=1; k<line->n_allele; k++)
                 maux->cnt[ maux->d[i][j].map[k] ]++;    // how many times an allele appears in the files
@@ -1899,6 +1898,7 @@ void merge_vcf(args_t *args)
 {
     args->out_fh  = hts_open(args->output_fname, hts_bcf_wmode(args->output_type));
     if ( args->out_fh == NULL ) error("Can't write to \"%s\": %s\n", args->output_fname, strerror(errno));
+    if ( args->n_threads ) hts_set_threads(args->out_fh, args->n_threads);
     args->out_hdr = bcf_hdr_init("w");
 
     if ( args->header_fname )
@@ -1911,7 +1911,7 @@ void merge_vcf(args_t *args)
         for (i=0; i<args->files->nreaders; i++)
         {
             char buf[10]; snprintf(buf,10,"%d",i+1);
-            bcf_hdr_merge(args->out_hdr, args->files->readers[i].header,buf,args->force_samples);
+            merge_headers(args->out_hdr, args->files->readers[i].header,buf,args->force_samples);
         }
         bcf_hdr_append_version(args->out_hdr, args->argc, args->argv, "bcftools_merge");
         bcf_hdr_sync(args->out_hdr);
@@ -1966,6 +1966,7 @@ static void usage(void)
     fprintf(stderr, "    -O, --output-type <b|u|z|v>        'b' compressed BCF; 'u' uncompressed BCF; 'z' compressed VCF; 'v' uncompressed VCF [v]\n");
     fprintf(stderr, "    -r, --regions <region>             restrict to comma-separated list of regions\n");
     fprintf(stderr, "    -R, --regions-file <file>          restrict to regions listed in a file\n");
+    fprintf(stderr, "        --threads <int>                number of extra output compression threads [0]\n");
     fprintf(stderr, "\n");
     exit(1);
 }
@@ -1978,24 +1979,26 @@ int main_vcfmerge(int argc, char *argv[])
     args->argc   = argc; args->argv = argv;
     args->output_fname = "-";
     args->output_type = FT_VCF;
+    args->n_threads = 0;
     args->collapse = COLLAPSE_BOTH;
     int regions_is_file = 0;
 
     static struct option loptions[] =
     {
-        {"help",0,0,'h'},
-        {"merge",1,0,'m'},
-        {"file-list",1,0,'l'},
-        {"apply-filters",1,0,'f'},
-        {"use-header",1,0,1},
-        {"print-header",0,0,2},
-        {"force-samples",0,0,3},
-        {"output",1,0,'o'},
-        {"output-type",1,0,'O'},
-        {"regions",1,0,'r'},
-        {"regions-file",1,0,'R'},
-        {"info-rules",1,0,'i'},
-        {0,0,0,0}
+        {"help",no_argument,NULL,'h'},
+        {"merge",required_argument,NULL,'m'},
+        {"file-list",required_argument,NULL,'l'},
+        {"apply-filters",required_argument,NULL,'f'},
+        {"use-header",required_argument,NULL,1},
+        {"print-header",no_argument,NULL,2},
+        {"force-samples",no_argument,NULL,3},
+        {"output",required_argument,NULL,'o'},
+        {"output-type",required_argument,NULL,'O'},
+        {"threads",required_argument,NULL,9},
+        {"regions",required_argument,NULL,'r'},
+        {"regions-file",required_argument,NULL,'R'},
+        {"info-rules",required_argument,NULL,'i'},
+        {NULL,0,NULL,0}
     };
     while ((c = getopt_long(argc, argv, "hm:f:r:R:o:O:i:l:",loptions,NULL)) >= 0) {
         switch (c) {
@@ -2028,6 +2031,7 @@ int main_vcfmerge(int argc, char *argv[])
             case  1 : args->header_fname = optarg; break;
             case  2 : args->header_only = 1; break;
             case  3 : args->force_samples = 1; break;
+            case  9 : args->n_threads = strtol(optarg, 0, 0); break;
             case 'h':
             case '?': usage();
             default: error("Unknown argument: %s\n", optarg);
diff --git a/vcfnorm.c b/vcfnorm.c
index 37b668b..732eca9 100644
--- a/vcfnorm.c
+++ b/vcfnorm.c
@@ -39,25 +39,11 @@ THE SOFTWARE.  */
 #define CHECK_REF_EXIT 0
 #define CHECK_REF_WARN 1
 #define CHECK_REF_SKIP 2
+#define CHECK_REF_FIX  4
 
 #define MROWS_SPLIT 1
 #define MROWS_MERGE  2
 
-typedef struct
-{
-    int32_t dir:4, val:28;
-}
-cell_t;
-typedef struct
-{
-    int nmat, nref, nseq;
-    int ipos, lref, lseq;
-    cell_t *mat;
-    char *ref, *seq;
-    int m_arr, *ipos_arr, *lref_arr, *lseq_arr;
-}
-aln_aux_t;
-
 // for -m+, mapping from allele indexes of a single input record
 // to allele indexes of output record
 typedef struct
@@ -68,7 +54,6 @@ map_t;
 
 typedef struct
 {
-    aln_aux_t aln;
     char *tseq, *seq;
     int mseq;
     bcf1_t **lines, **tmp_lines, **alines, **blines, *mrow_out;
@@ -76,7 +61,7 @@ typedef struct
     map_t *maps;     // mrow map for each buffered record
     char **als;
     int mmaps, nals, mals;
-    uint8_t *tmp_arr1, *tmp_arr2;
+    uint8_t *tmp_arr1, *tmp_arr2, *diploid;
     int ntmp_arr1, ntmp_arr2;
     kstring_t *tmp_str;
     kstring_t *tmp_als, tmp_als_str;
@@ -87,502 +72,227 @@ typedef struct
     bcf_srs_t *files;       // using the synced reader only for -r option
     bcf_hdr_t *hdr;
     faidx_t *fai;
+    struct { int tot, set, swap; } nref;
     char **argv, *output_fname, *ref_fname, *vcf_fname, *region, *targets;
-    int argc, rmdup, output_type, check_ref, strict_filter;
-    int nchanged, nskipped, ntotal, mrows_op, mrows_collapse, parsimonious;
+    int argc, rmdup, output_type, n_threads, check_ref, strict_filter, do_indels;
+    int nchanged, nskipped, nsplit, ntotal, mrows_op, mrows_collapse, parsimonious;
 }
 args_t;
 
-#if OLD_WAY
-void _vcfnorm_debug_print(aln_aux_t *aux)
+static inline int replace_iupac_codes(char *seq, int nseq)
 {
-    cell_t *mat = aux->mat;
-    char *ref = aux->ref;
-    char *seq = aux->seq;
-    int nref  = aux->nref;
-    int nseq  = aux->nseq;
-    int k     = (nref+1)*(nseq+1)-1;
-    int kd    = nref+2;
-    int i = k/(nref+1);
-    int j = k - i*(nref+1);
-    assert(i>0 && j>0);
-    int l = k, ialn = 0, nout_ref = 0, nout_seq = 0, ipos = 0;
-    char *aln_ref = (char*) malloc(sizeof(char)*(k+1));
-    char *aln_seq = (char*) malloc(sizeof(char)*(k+1));
-    while ( l>0 )
-    {
-        if ( j<=0 || mat[l].dir==1 )    // i
-        {
-            aln_ref[ialn] = '-';
-            aln_seq[ialn] = seq[nseq-i];
-            ipos = 0;
-            nout_seq++;
-            l -= kd - 1;
-            i--;
-        }
-        else if ( i<=0 || mat[l].dir==-1 )  // d
-        {
-            aln_ref[ialn] = ref[nref-j];
-            aln_seq[ialn] = '-';
-            ipos = 0;
-            nout_ref++;
-            l--;
-            j--;
-        }
-        else     // match or mismatch
-        {
-            aln_ref[ialn] = ref[nref-j];
-            aln_seq[ialn] = seq[nseq-i];
-            ipos = ref[nref-j+1]==seq[nseq-i+1] ? ipos+1 : 1;
-            nout_seq++;
-            nout_ref++;
-            l -= kd;
-            i--;
-            j--;
-        }
-        ialn++;
-    }
-    aln_ref[ialn] = aln_seq[ialn] = 0;
-    fprintf(stderr, "ref: %s\n", ref);
-    fprintf(stderr, "seq: %s\n", seq);
-    fprintf(stderr, "-> %s\n", aln_ref);
-    fprintf(stderr, "-> %s\n", aln_seq);
-    free(aln_ref);
-    free(aln_seq);
-
-    fprintf(stderr, "      ");
-    for (j=0; j<nref; j++) fprintf(stderr, "   %c ", ref[nref-j-1]); fprintf(stderr, "\n");
-    for (i=0; i<=nseq; i++)
-    {
-        fprintf(stderr, "%c", i==0 ? ' ' : seq[nseq-i]);
-        for (j=0; j<=nref; j++)
-        {
-            char dir = ' ';
-            if ( mat[i*(nref+1)+j].dir==1 ) dir = 'i';
-            else if ( mat[i*(nref+1)+j].dir==-1 ) dir = 'd';
-            fprintf(stderr, " %3d%c", (int)mat[i*(nref+1)+j].val, dir);
-        }
-        fprintf(stderr,"\n");
+    // Replace ambiguity codes with N for now, it awaits to be seen what the VCF spec codifies in the end
+    int i, n = 0;
+    for (i=0; i<nseq; i++)
+    {
+        char c = toupper(seq[i]);
+        if ( c!='A' && c!='C' && c!='G' && c!='T' ) { seq[i] = 'N'; n++; }
     }
+    return n;
 }
 
-static int align(args_t *args, aln_aux_t *aux)
+static void fix_ref(args_t *args, bcf1_t *line)
 {
-    // Needleman-Wunsch global alignment. Note that the sequences are aligned from
-    //  the end where matches are preferred, gaps are pushed to the front (left-aligned)
-    char *ref = aux->ref;
-    char *seq = aux->seq;
-    int nref  = aux->nref;
-    int nseq  = aux->nseq;
-    if ( (nref+1)*(nseq+1) > aux->nmat )
-    {
-        aux->nmat = (nref+1)*(nseq+1);
-        aux->mat  = (cell_t *) realloc(aux->mat, sizeof(cell_t)*aux->nmat);
-        if ( !aux->mat )
-            error("Could not allocate %ld bytes of memory at %d\n", sizeof(cell_t)*aux->nmat, args->files->readers[0].buffer[0]->pos+1);
-    }
-    const int GAP_OPEN = -1, GAP_CLOSE = -1, GAP_EXT = 0, MATCH = 1, MISM = -1, DI = 1, DD = -1, DM = 0;
-    cell_t *mat = aux->mat;
-    int i, j, k = nref+2, kd = nref+2;
-    mat[0].val = 20; mat[0].dir = DM;   // the last ref and alt bases match
-    for (j=1; j<=nref; j++) { mat[j].val = 0; mat[j].dir = DM; }
-    for (i=1; i<=nseq; i++)
-    {
-        mat[k-1].val = 0;
-        mat[k-1].dir = DM;
-        int jmax = i-1 < nref ? i-1 : nref;
-        for (j=1; j<=jmax; j++)
-        {
-            // prefer insertions to deletions and mismatches
-            int max, dir, score;
-            if ( ref[nref-j]==seq[nseq-i] )
-            {
-                // match
-                max = mat[k-kd].val + MATCH;
-                if ( mat[k-kd].dir!=DM ) max += GAP_CLOSE;
-                dir = DM;
-
-                // insertion
-                score = mat[k-kd+1].dir == DI ? mat[k-kd+1].val + GAP_EXT: mat[k-kd+1].val + GAP_OPEN;
-                if ( max < score )  { max = score; dir = DI; }
-
-                // deletion
-                score = mat[k-1].dir == DD ? mat[k-1].val + GAP_EXT : mat[k-1].val + GAP_OPEN;
-                if ( max < score ) { max = score; dir = DD; }
-            }
-            else
-            {
-                // insertion
-                max = mat[k-kd+1].dir == DI ? mat[k-kd+1].val + GAP_EXT : mat[k-kd+1].val + GAP_OPEN;
-                dir = DI;
-
-                // deletion
-                score = mat[k-1].dir == DD ? mat[k-1].val + GAP_EXT : mat[k-1].val + GAP_OPEN;
-                if ( max < score ) { max = score; dir = DD; }
-
-                // mismatch
-                score = mat[k-kd].val + MISM;
-                if ( mat[k-kd].dir!=DM ) score += GAP_CLOSE;
-                if ( max < score ) { max = score; dir = DM; }
-            }
-            mat[k].val = max;
-            mat[k].dir = dir;
-            k++;
-        }
-        for (j=jmax+1; j<=nref; j++)
-        {
-            // prefer deletions to insertions and mismatches
-            int max, dir, score;
-            if ( ref[nref-j]==seq[nseq-i] )
-            {
-                // match
-                max = mat[k-kd].val + MATCH;
-                if ( mat[k-kd].dir!=DM ) max += GAP_CLOSE;
-                dir = DM;
-
-                // deletion
-                score = mat[k-1].dir == DD ? mat[k-1].val + GAP_EXT: mat[k-1].val + GAP_OPEN;
-                if ( max < score ) { max = score; dir = DD; }
-
-                // insertion
-                score = mat[k-kd+1].dir == DI ? mat[k-kd+1].val + GAP_EXT : mat[k-kd+1].val + GAP_OPEN;
-                if ( max < score )  { max = score; dir = DI; }
-            }
-            else
-            {
-                // deletion
-                max = mat[k-1].dir == DD ? mat[k-1].val + GAP_EXT : mat[k-1].val + GAP_OPEN;
-                dir = DD;
-
-                // insertion
-                score = mat[k-kd+1].dir == DI ? mat[k-kd+1].val + GAP_EXT : mat[k-kd+1].val + GAP_OPEN;
-                if ( max < score ) { max = score; dir = DI; }
-
-                // mismatch
-                score = mat[k-kd].val + MISM;
-                if ( mat[k-kd].dir!=DM ) score += GAP_CLOSE;
-                if ( max < score ) { max = score; dir = DM; }
-            }
-            mat[k].val = max;
-            mat[k].dir = dir;
-            k++;
-        }
-        k++;
+    int reflen = strlen(line->d.allele[0]);
+    int i, maxlen = reflen, len;
+    for (i=1; i<line->n_allele; i++)
+    {
+        int len = strlen(line->d.allele[i]);
+        if ( maxlen < len ) maxlen = len;
     }
 
-    // _vcfnorm_debug_print(aux);
+    char *ref = faidx_fetch_seq(args->fai, (char*)bcf_seqname(args->hdr,line), line->pos, line->pos+maxlen-1, &len);
+    if ( !ref ) error("faidx_fetch_seq failed at %s:%d\n", bcf_seqname(args->hdr,line),line->pos+1);
+    replace_iupac_codes(ref,len);
 
-    // Skip as much of the matching sequence at the beggining as possible. (Note, the sequence
-    // is reversed, thus skipping from the end.)
-    k = (nref+1)*(nseq+1)-1;
-    int kmin = nref>nseq ? 2*(nref+1) - nseq : (nseq-nref)*(nref+1);    // skip the first row and column of the matrix, which are 0s
-    int ipos = 0;
-    while (k>kmin && mat[k].dir==DM && ref[ipos]==seq[ipos]) { k -= kd; ipos++; }
+    args->nref.tot++;
 
-    i = k/(nref+1);             // seq[nseq-i]
-    j = k - i*(nref+1);         // ref[nref-j]
+    // is the REF different?
+    if ( !strncasecmp(line->d.allele[0],ref,reflen) ) { free(ref); return; }
 
-    if ( !i && !j )
-    {
-        // no gaps: this is a legitimate case, consider MNPs
-        int l = 0;
-        while ( l<nseq && l<nref && ref[l]==seq[l] ) l++;
-        if ( l==nseq || l==nref ) return -2;    // ALT is identical to REF
-        assert( l>0 );
-        while ( ipos>l && ref[ipos]==seq[ipos] ) ipos--;
-        aux->ipos = l;          // position of the last matching base (buffer coordinates)
-        aux->lref = ipos + 1;   // position of the first base in the suffix
-        aux->lseq = ipos + 1;
-        return 0;
+    // is the REF allele missing or N?
+    if ( reflen==1 && (line->d.allele[0][0]=='.' || line->d.allele[0][0]=='N' || line->d.allele[0][0]=='n') ) 
+    { 
+        line->d.allele[0][0] = ref[0]; 
+        args->nref.set++; 
+        free(ref);
+        bcf_update_alleles(args->hdr,line,(const char**)line->d.allele,line->n_allele);
+        return;
     }
-    assert(i>0 && j>0);
 
-    int l = k, nout_ref = ipos, nout_seq = ipos, nsuffix = 0;
-    while ( l>0 )
+    // does REF contain non-standard bases?
+    if ( replace_iupac_codes(line->d.allele[0],strlen(line->d.allele[0])) )
     {
-        if ( j<=0 || mat[l].dir==DI )    // insertion
-        {
-            nsuffix = 0;
-            nout_seq++;
-            l -= kd - 1;
-            i--;
-        }
-        else if ( i<=0 || mat[l].dir==DD )  // deletion
-        {
-            nsuffix = 0;
-            nout_ref++;
-            l--;
-            j--;
-        }
-        else     // match/mismatch
-        {
-            nsuffix = ref[nref-j]==seq[nseq-i] ? nsuffix + 1 : 0;
-            nout_seq++;
-            nout_ref++;
-            l -= kd;
-            i--;
-            j--;
-        }
+        args->nref.set++;
+        bcf_update_alleles(args->hdr,line,(const char**)line->d.allele,line->n_allele);
+        if ( !strncasecmp(line->d.allele[0],ref,reflen) ) { free(ref); return; }
     }
-    if ( !ipos ) return -1; // the window is too small
-
-    aux->ipos = ipos - 1;
-    aux->lref = nout_ref - nsuffix;
-    aux->lseq = nout_seq - nsuffix;
-
-    // The indels and complex events do not have to be padded
-    if ( aux->lref - aux->ipos > 1 && aux->lseq - aux->ipos > 1 && ref[aux->ipos]==seq[aux->ipos] ) aux->ipos++;
-    return 0;
-}
-
-int realign(args_t *args, bcf1_t *line)
-{
-    bcf_unpack(line, BCF_UN_STR);
 
-    char *tmp;
-    int i, ref_len = strlen(line->d.allele[0]), len = ref_len;
+    // is it swapped?
     for (i=1; i<line->n_allele; i++)
     {
-        int l = strlen(line->d.allele[i]);
-        if ( len < l ) len = l;
-    }
-    for (i=0; i<line->n_allele; i++)
-    {
-        tmp = line->d.allele[i];
-        while (*tmp) { *tmp = toupper(*tmp); tmp++; }
+        int len = strlen(line->d.allele[i]);
+        if ( !strncasecmp(line->d.allele[i],ref,len) ) break;
     }
 
-    int ref_winlen;
-    char *ref = NULL;
-    if ( len==1 || line->n_allele==1 )
+    kstring_t str = {0,0,0};
+    if ( i==line->n_allele )
     {
-        // SNP
-        int reflen = strlen(line->d.allele[0]);
-        ref = faidx_fetch_seq(args->fai, (char*)args->hdr->id[BCF_DT_CTG][line->rid].key, line->pos, line->pos+reflen-1, &ref_winlen);
-        if ( !ref ) error("faidx_fetch_seq failed at %s:%d\n", args->hdr->id[BCF_DT_CTG][line->rid].key, line->pos+1);
-        if ( !strncmp(ref,line->d.allele[0],reflen) )
+        // none of the alternate alleles matches the reference
+        if ( line->n_allele>1 )
+            args->nref.set++;
+        else
+            args->nref.swap++;
+
+        kputs(line->d.allele[0],&str);
+        kputc(',',&str);
+        for (i=1; i<line->n_allele; i++)
         {
-            free(ref);
-            return 0;
+            kputs(line->d.allele[i],&str);
+            kputc(',',&str);
         }
-        if ( args->check_ref==CHECK_REF_EXIT )
-            error("Reference allele mismatch at %s:%d .. '%c' vs '%c'\n", bcf_seqname(args->hdr,line),line->pos+1,ref[0],line->d.allele[0][0]);
-        if ( args->check_ref & CHECK_REF_WARN )
-            fprintf(stderr,"REF_MISMATCH\t%s\t%d\t%s\n", bcf_seqname(args->hdr,line),line->pos+1,line->d.allele[0]);
-        free(ref);
-        return -1;
+        kputc(ref[0],&str);
+        bcf_update_alleles_str(args->hdr,line,str.s);
+        str.l = 0;
     }
+    else
+        args->nref.swap++;
+    free(ref);
 
-    // Sanity check: exclude broken VCFs with long stretches of N's
-    if ( len>1000 )
+    // swap the alleles
+    int j;
+    kputs(line->d.allele[i],&str);
+    for (j=1; j<i; j++)
     {
-        for (i=0; i<ref_len; i++)
-            if ( line->d.allele[0][i]=='N' ) return -1;
+        kputc(',',&str);
+        kputs(line->d.allele[j],&str);
     }
-
-    int win = line->pos < args->aln_win ? line->pos : args->aln_win;
-    len += win + 2;
-    if ( args->mseq < len*(line->n_allele-1) )
+    kputc(',',&str);
+    kputs(line->d.allele[0],&str);
+    for (j=i+1; j<line->n_allele; j++)
     {
-        args->mseq = len*(line->n_allele-1);
-        args->seq  = (char*) realloc(args->seq, sizeof(char)*args->mseq);
-    }
-    ref = faidx_fetch_seq(args->fai, (char*)args->hdr->id[BCF_DT_CTG][line->rid].key, line->pos-win, line->pos+ref_len, &ref_winlen);
-    if ( !ref ) error("faidx_fetch_seq failed at %s:%d\n", args->hdr->id[BCF_DT_CTG][line->rid].key, line->pos-win);
-    assert( ref_winlen==ref_len+win+1 );
-
-    for (i=0; i<ref_len; i++) ref[i] = toupper(ref[i]);
-
-    // Sanity check: the reference sequence must match the REF allele
-    if ( strncmp(&ref[win],line->d.allele[0],ref_len) )
-    {
-        for (i=0; i<ref_len; i++)
-            if ( ref[win+i]!=line->d.allele[0][i] ) break;
-        if ( args->check_ref==CHECK_REF_EXIT )
-            error("\nSanity check failed, the reference sequence differs at %s:%d[%d] .. '%c' vs '%c'\n",
-                    args->hdr->id[BCF_DT_CTG][line->rid].key, line->pos+1, i+1,ref[win+i],line->d.allele[0][i]);
-        if ( args->check_ref & CHECK_REF_WARN )
-            fprintf(stderr,"REF_MISMATCH\t%s\t%d\t%s\n", bcf_seqname(args->hdr,line),line->pos+1,line->d.allele[0]);
-        free(ref);
-        return -1;
-    }
-
-    if ( args->aln.m_arr < line->n_allele )
+        kputc(',',&str);
+        kputs(line->d.allele[j],&str);
+    }
+    bcf_update_alleles_str(args->hdr,line,str.s);
+
+    // swap genotypes
+    int ntmp = args->ntmp_arr1 / sizeof(int32_t); // reuse tmp_arr declared as uint8_t
+    int ngts = bcf_get_genotypes(args->hdr, line, &args->tmp_arr1, &ntmp);
+    args->ntmp_arr1 = ntmp * sizeof(int32_t);
+    int32_t *gts = (int32_t*) args->tmp_arr1;
+    int ni = 0;
+    for (j=0; j<ngts; j++)
     {
-        args->aln.m_arr = line->n_allele;
-        args->aln.ipos_arr = (int*) realloc(args->aln.ipos_arr, sizeof(int)*args->aln.m_arr);
-        args->aln.lref_arr = (int*) realloc(args->aln.lref_arr, sizeof(int)*args->aln.m_arr);
-        args->aln.lseq_arr = (int*) realloc(args->aln.lseq_arr, sizeof(int)*args->aln.m_arr);
+        if ( gts[j]==bcf_gt_unphased(0) ) { gts[j] = bcf_gt_unphased(i); ni++; }
+        else if ( gts[j]==bcf_gt_phased(0) ) { gts[j] = bcf_gt_phased(i); ni++; }
+        else if ( gts[j]==bcf_gt_unphased(i) ) gts[j] = bcf_gt_unphased(0);
+        else if ( gts[j]==bcf_gt_phased(i) ) gts[j] = bcf_gt_phased(0);
     }
-    int *ipos = args->aln.ipos_arr;
-    int *iref = args->aln.lref_arr;
-    int *iseq = args->aln.lseq_arr;
-    int min_pos = INT_MAX, max_ref = 0;
+    bcf_update_genotypes(args->hdr,line,gts,ngts);
 
-    static int aln_win_warned = 0;
-    int j, k;
-    for (j=1; j<line->n_allele; j++)
+    // update AC
+    int nac = bcf_get_info_int32(args->hdr, line, "AC", &args->tmp_arr1, &ntmp);
+    args->ntmp_arr1 = ntmp * sizeof(int32_t);
+    if ( i <= nac )
     {
-        // get the ALT ready for alignment
-        args->tseq = args->seq + (j-1)*len;
-        for (i=0; i<win; i++) args->tseq[i] = ref[i];
-        char *t = line->d.allele[j];
-        while (*t) { args->tseq[i++] = *t; t++; }
-        args->tseq[i++] = ref[ref_winlen-1];
-        args->tseq[i]   = 0;
-
-        args->aln.ref  = ref;
-        args->aln.seq  = args->tseq;
-        args->aln.nref = ref_winlen;    // reflen which goes into realignment: VCF ref + #win bases which precede
-        args->aln.nseq = i;             // same as reflen but for alt
-
-        int ret = align(args, &args->aln);
-        if ( ret<0 )
-        {
-            free(ref);
-            if ( ret==-1 )
-            {
-                // todo: better error analysis, see 2:1 in test/norm.vcf
-                // fprintf(stderr,"Warning: The -w alignment window too small for %s:%d\n", bcf_seqname(args->hdr,line),line->pos+1);
-                return 0;   // leave as is
-            }
-            if ( ret==-2 ) fprintf(stderr,"Warning: REF allele is identical to ALT at %s:%d\n", bcf_seqname(args->hdr,line),line->pos+1);
-            return -1;
-        }
-
-        #if 0
-            fprintf(stderr, "%s  \t nref=%d\n", ref, ref_winlen);
-            fprintf(stderr, "%s  \t nseq=%d\n", args->tseq, i);
-            fprintf(stderr, "pos=%d win=%d  ipos=%d lref=%d lseq=%d\n", line->pos+1, win, args->aln.ipos, args->aln.lref, args->aln.lseq);
-            fprintf(stderr, "-> "); for (k=args->aln.ipos; k<args->aln.lref; k++) fprintf(stderr, "%c", ref[k]); fprintf(stderr, "\n");
-            fprintf(stderr, "-> "); for (k=args->aln.ipos; k<args->aln.lseq; k++) fprintf(stderr, "%c", args->tseq[k]); fprintf(stderr, "\n");
-            fprintf(stderr, "\n");
-        #endif
-
-        if ( !args->aln.ipos && !aln_win_warned )
-        {
-            fprintf(stderr,"Warning: bigger -w is needed [todo: improve me, %s:%d %s,%s]\n",
-                    bcf_seqname(args->hdr,line),line->pos+1, line->d.allele[0],line->d.allele[j]);
-            aln_win_warned = 1;
-        }
-        ipos[j] = args->aln.ipos;   // 0-based position before the first difference (w.r.t. the window)
-        iref[j] = args->aln.lref;   // length of the REF alignment (or the index after the last aligned position)
-        iseq[j] = args->aln.lseq;
-        if ( max_ref < iref[j] ) max_ref = iref[j];
-        if ( min_pos > ipos[j] ) min_pos = ipos[j];
-        assert( iseq[j]<=len );
+        int32_t *ac = (int32_t*)args->tmp_arr1;
+        ac[i-1] = ni;
+        bcf_update_info_int32(args->hdr, line, "AC", ac, nac);
     }
+    
+    free(str.s);
+}
 
-    // Check if the record's position must be changed
-    int nmv = win - min_pos;
-    // This assertion that we will never want align more to the right is too
-    // strong, consider cases like GATG -> GACT
-    //  assert( nmv>=0 );
-    line->pos -= nmv;
-
-    hts_expand0(kstring_t,line->n_allele,args->ntmp_als,args->tmp_als);
-    // REF
-    args->tmp_als[0].l = 0;
-    kputsn(&ref[min_pos], max_ref-min_pos, &args->tmp_als[0]);
-    // ALTs
-    int min_len = args->tmp_als[0].l;
-    for (k=1; k<line->n_allele; k++)
-    {
-        args->tmp_als[k].l = 0;
-
-        // prefix the sequence with REF bases if the other alleles were aligned more to the left
-        int nprefix = ipos[k] - min_pos;
-        if ( nprefix ) kputsn(&ref[min_pos], nprefix, &args->tmp_als[k]);
-
-        // the ALT sequence
-        int nseq = iseq[k] - ipos[k];
-        if ( nseq )
-        {
-            char *alt = args->seq + (k-1)*len + ipos[k];
-            kputsn(alt, nseq, &args->tmp_als[k]);
-        }
-
-        // suffix invoked by other deletions which must be added to match the REF
-        int nsuffix = max_ref - iref[k];
-        if ( nsuffix ) kputsn(&ref[iref[k]], nsuffix, &args->tmp_als[k]);
-
-        if ( min_len > args->tmp_als[k].l ) min_len = args->tmp_als[k].l;
-    }
-    free(ref);
+static void fix_dup_alt(args_t *args, bcf1_t *line)
+{
+    // update alleles, create a mapping between old and new indexes
+    hts_expand(uint8_t,line->n_allele,args->ntmp_arr1,args->tmp_arr1);
+    args->tmp_arr1[0] = 0;  // ref always unchanged
 
-    // create new block of alleles
-    args->tmp_als_str.l = 0;
-    if ( args->parsimonious )
+    int i, j, nals = line->n_allele, nals_ori = line->n_allele;
+    for (i=1, j=1; i<line->n_allele; i++)
     {
-        // check if we can trim from the left
-        for (i=0; i<args->tmp_als[0].l; i++)
-        {
-            for (k=1; k<line->n_allele; k++)
-                if ( args->tmp_als[0].s[i]!=args->tmp_als[k].s[i] ) break;
-            if ( k!=line->n_allele ) break;
-        }
-        if ( i>=min_len ) i = min_len - 1;
-        if ( i>0 )  // can be left trimmed
+        if ( strcmp(line->d.allele[0],line->d.allele[i]) )
         {
-            for (k=0; k<line->n_allele; k++)
-            {
-                if (k>0) kputc(',',&args->tmp_als_str);
-                kputsn(args->tmp_als[k].s+i,args->tmp_als[k].l-i,&args->tmp_als_str);
-            }
-            kputc(0,&args->tmp_als_str);
-            line->pos += i;
+            args->tmp_arr1[i] = j++;
+            continue;
         }
-        // if REF allele has not changed, ALTs must be unchanged as well
-        else if ( !strcmp(line->d.allele[0],args->tmp_als[0].s) ) return 1;
+        args->tmp_arr1[i] = 0;
+        nals--;
     }
-    else if ( !strcmp(line->d.allele[0],args->tmp_als[0].s) ) return 1;
-    if ( !args->tmp_als_str.l )
+    for (i=1, j=1; i<line->n_allele; i++)
     {
-        for (k=0; k<line->n_allele; k++)
-        {
-            if (k>0) kputc(',',&args->tmp_als_str);
-            kputsn(args->tmp_als[k].s,args->tmp_als[k].l,&args->tmp_als_str);
-        }
+        if ( !args->tmp_arr1[i] ) continue;
+        line->d.allele[j++] = line->d.allele[i];
     }
-    args->nchanged++;
-    bcf_update_alleles_str(args->hdr,line,args->tmp_als_str.s);
+    bcf_update_alleles(args->hdr, line, (const char**)line->d.allele, nals);
 
-    return 1;
+
+    // update genotypes
+    int ntmp = args->ntmp_arr2 / sizeof(int32_t); // reuse tmp_arr declared as uint8_t
+    int ngts = bcf_get_genotypes(args->hdr, line, &args->tmp_arr2, &ntmp);
+    args->ntmp_arr2 = ntmp * sizeof(int32_t);
+    int32_t *gts = (int32_t*) args->tmp_arr2;
+    int changed = 0;
+    for (i=0; i<ngts; i++)
+    {
+        if ( bcf_gt_is_missing(gts[i]) || gts[i]==bcf_int32_vector_end ) continue;
+        int ial = bcf_gt_allele(gts[i]);
+        if ( ial<nals_ori && ial==args->tmp_arr1[ial] ) continue;
+        int ial_new = ial<nals_ori ? args->tmp_arr1[ial] : 0;
+        gts[i] = bcf_gt_is_phased(gts[i]) ? bcf_gt_phased(ial_new) : bcf_gt_unphased(ial_new);
+        changed = 1;
+    }
+    if ( changed ) bcf_update_genotypes(args->hdr,line,gts,ngts);
 }
-#else
+
+#define ERR_DUP_ALLELE      -2
+#define ERR_REF_MISMATCH    -1
+#define ERR_OK              0
+#define ERR_SYMBOLIC        1
 
 static int realign(args_t *args, bcf1_t *line)
 {
     bcf_unpack(line, BCF_UN_STR);
 
     // Sanity check REF
-    int nref, reflen = strlen(line->d.allele[0]);
+    int i, nref, reflen = strlen(line->d.allele[0]);
     char *ref = faidx_fetch_seq(args->fai, (char*)args->hdr->id[BCF_DT_CTG][line->rid].key, line->pos, line->pos+reflen-1, &nref);
     if ( !ref ) error("faidx_fetch_seq failed at %s:%d\n", args->hdr->id[BCF_DT_CTG][line->rid].key, line->pos+1);
+    replace_iupac_codes(ref,nref);
+
+    // does REF contain non-standard bases?
+    if ( replace_iupac_codes(line->d.allele[0],reflen) )
+    {
+        args->nchanged++;
+        bcf_update_alleles(args->hdr,line,(const char**)line->d.allele,line->n_allele);
+    }
     if ( strcasecmp(ref,line->d.allele[0]) )
     {
         if ( args->check_ref==CHECK_REF_EXIT )
-            error("Reference allele mismatch at %s:%d .. '%s' vs '%s'\n", bcf_seqname(args->hdr,line),line->pos+1,ref,line->d.allele[0]);
+            error("Reference allele mismatch at %s:%d .. REF_SEQ:'%s' vs VCF:'%s'\n", bcf_seqname(args->hdr,line),line->pos+1,ref,line->d.allele[0]);
         if ( args->check_ref & CHECK_REF_WARN )
             fprintf(stderr,"REF_MISMATCH\t%s\t%d\t%s\n", bcf_seqname(args->hdr,line),line->pos+1,line->d.allele[0]);
         free(ref);
-        return -1;
+        return ERR_REF_MISMATCH;
     }
     free(ref);
     ref = NULL;
 
-    if ( line->n_allele == 1 ) return 0;    // a REF
+    if ( line->n_allele == 1 ) return ERR_OK;    // a REF
 
     // make a copy of each allele for trimming
-    int i;
     hts_expand0(kstring_t,line->n_allele,args->ntmp_als,args->tmp_als);
     kstring_t *als = args->tmp_als;
     for (i=0; i<line->n_allele; i++)
     {
-        if ( line->d.allele[i][0]=='<' ) return 0;  // symbolic allele
+        if ( line->d.allele[i][0]=='<' ) return ERR_SYMBOLIC;  // symbolic allele
 
         als[i].l = 0;
         kputs(line->d.allele[i], &als[i]);
+
+        if ( i>0 && als[i].l==als[0].l && !strcasecmp(als[0].s,als[i].s) ) return ERR_DUP_ALLELE;
     }
 
 
@@ -609,6 +319,7 @@ static int realign(args_t *args, bcf1_t *line)
             free(ref);
             ref = faidx_fetch_seq(args->fai, (char*)args->hdr->id[BCF_DT_CTG][line->rid].key, line->pos-npad, line->pos-1, &nref);
             if ( !ref ) error("faidx_fetch_seq failed at %s:%d\n", args->hdr->id[BCF_DT_CTG][line->rid].key, line->pos-npad+1);
+            replace_iupac_codes(ref,nref);
             for (i=0; i<line->n_allele; i++)
             {
                 ks_resize(&als[i], als[i].l + npad);
@@ -647,7 +358,7 @@ static int realign(args_t *args, bcf1_t *line)
 
     // Have the alleles changed?
     als[0].s[ als[0].l ] = 0;  // in order for strcmp to work
-    if ( ori_pos==line->pos && !strcasecmp(line->d.allele[0],als[0].s) ) return 1;
+    if ( ori_pos==line->pos && !strcasecmp(line->d.allele[0],als[0].s) ) return ERR_OK;
 
     // Create new block of alleles and update
     args->tmp_als_str.l = 0;
@@ -660,11 +371,9 @@ static int realign(args_t *args, bcf1_t *line)
     bcf_update_alleles_str(args->hdr,line,args->tmp_als_str.s);
     args->nchanged++;
 
-    return 1;
+    return ERR_OK;
 }
 
-#endif
-
 static void split_info_numeric(args_t *args, bcf1_t *src, bcf_info_t *info, int ialt, bcf1_t *dst)
 {
     #define BRANCH_NUMERIC(type,type_t) \
@@ -1014,7 +723,7 @@ static void split_multiallelic_to_biallelics(args_t *args, bcf1_t *line)
     {
         args->tmp_lines = (bcf1_t **)realloc(args->tmp_lines,sizeof(bcf1_t*)*args->ntmp_lines);
         for (i=args->mtmp_lines; i<args->ntmp_lines; i++)
-            args->tmp_lines[i] = bcf_init1();
+            args->tmp_lines[i] = NULL;
         args->mtmp_lines = args->ntmp_lines;
     }
     kstring_t tmp = {0,0,0};
@@ -1024,6 +733,7 @@ static void split_multiallelic_to_biallelics(args_t *args, bcf1_t *line)
     int gt_id = bcf_hdr_id2int(args->hdr,BCF_DT_ID,"GT");
     for (i=0; i<args->ntmp_lines; i++)  // for each ALT allele
     {
+        if ( !args->tmp_lines[i] ) args->tmp_lines[i] = bcf_init1();
         bcf1_t *dst = args->tmp_lines[i];
         bcf_clear(dst);
 
@@ -1031,6 +741,10 @@ static void split_multiallelic_to_biallelics(args_t *args, bcf1_t *line)
         dst->pos  = line->pos;
         dst->qual = line->qual;
 
+        // Not quite sure how to handle IDs, they can be assigned to a specific
+        // ALT.  For now we leave the ID unchanged for all.
+        bcf_update_id(args->hdr, dst, line->d.id ? line->d.id : ".");
+
         tmp.l = rlen;
         kputs(line->d.allele[i+1],&tmp);
         bcf_update_alleles_str(args->hdr,dst,tmp.s);
@@ -1089,7 +803,8 @@ static void merge_info_numeric(args_t *args, bcf1_t **lines, int nlines, bcf_inf
         int i,k,len = bcf_hdr_id2length(args->hdr,BCF_HL_INFO,info->key);  \
         if ( len==BCF_VL_A ) \
         { \
-            assert( nvals_ori==lines[0]->n_allele - 1); \
+            if (nvals_ori!=lines[0]->n_allele - 1) \
+                error("vcfnorm: number of fields in first record at position %s:%d for INFO tag %s not as expected [found: %d vs expected:%d]\n", bcf_seqname(args->hdr,lines[0]),lines[0]->pos+1, tag, nvals_ori, lines[0]->n_allele-1); \
             int nvals = dst->n_allele - 1; \
             ENLARGE_ARRAY(type_t,set_missing,args->tmp_arr1,args->ntmp_arr1,1,nvals_ori,nvals); \
             vals = (type_t*) args->tmp_arr1; \
@@ -1097,8 +812,10 @@ static void merge_info_numeric(args_t *args, bcf1_t **lines, int nlines, bcf_inf
             { \
                 int ntmp2 = args->ntmp_arr2 / sizeof(type_t); \
                 int nvals2 = bcf_get_info_##type(args->hdr,lines[i],tag,&args->tmp_arr2,&ntmp2); \
+                if (nvals2<0) continue; /* info tag does not exist in this record, skip */ \
                 args->ntmp_arr2 = ntmp2 * sizeof(type_t); \
-                assert( nvals2==lines[i]->n_allele-1 ); \
+                if (nvals2!=lines[i]->n_allele-1) \
+                    error("vcfnorm: could not merge INFO tag %s at position %s:%d\n", tag, bcf_seqname(args->hdr,lines[i]),lines[i]->pos+1); \
                 vals2 = (type_t*) args->tmp_arr2; \
                 for (k=0; k<nvals2; k++) \
                 { \
@@ -1110,7 +827,8 @@ static void merge_info_numeric(args_t *args, bcf1_t **lines, int nlines, bcf_inf
         } \
         else if ( len==BCF_VL_R ) \
         { \
-            assert( nvals_ori==lines[0]->n_allele ); \
+            if (nvals_ori!=lines[0]->n_allele) \
+                error("vcfnorm: number of fields in first record at position %s:%d for INFO tag %s not as expected [found: %d vs expected:%d]\n", bcf_seqname(args->hdr,lines[0]),lines[0]->pos+1, tag, nvals_ori, lines[0]->n_allele); \
             int nvals = dst->n_allele; \
             ENLARGE_ARRAY(type_t,set_missing,args->tmp_arr1,args->ntmp_arr1,1,nvals_ori,nvals); \
             vals = (type_t*) args->tmp_arr1; \
@@ -1118,8 +836,10 @@ static void merge_info_numeric(args_t *args, bcf1_t **lines, int nlines, bcf_inf
             { \
                 int ntmp2 = args->ntmp_arr2 / sizeof(type_t); \
                 int nvals2 = bcf_get_info_##type(args->hdr,lines[i],tag,&args->tmp_arr2,&ntmp2); \
+                if (nvals2<0) continue; /* info tag does not exist in this record, skip */ \
                 args->ntmp_arr2 = ntmp2 * sizeof(type_t); \
-                assert( nvals2==lines[i]->n_allele ); \
+                if (nvals2!=lines[i]->n_allele) \
+                    error("vcfnorm: could not merge INFO tag %s at position %s:%d\n", tag, bcf_seqname(args->hdr,lines[i]),lines[i]->pos+1); \
                 vals2 = (type_t*) args->tmp_arr2; \
                 for (k=0; k<nvals2; k++) \
                 { \
@@ -1131,7 +851,11 @@ static void merge_info_numeric(args_t *args, bcf1_t **lines, int nlines, bcf_inf
         } \
         else if ( len==BCF_VL_G ) \
         { \
-            assert( nvals_ori==lines[0]->n_allele*(lines[0]->n_allele+1)/2 );   /* expecting diploid gt in INFO */ \
+            /* expecting diploid gt in INFO */ \
+            if (nvals_ori!=lines[0]->n_allele*(lines[0]->n_allele+1)/2) { \
+                fprintf(stderr, "todo: merge Number=G INFO fields for haploid sites\n"); \
+                error("vcfnorm: number of fields in first record at position %s:%d for INFO tag %s not as expected [found: %d vs expected:%d]\n", bcf_seqname(args->hdr,lines[0]),lines[0]->pos+1, tag, nvals_ori, lines[0]->n_allele*(lines[0]->n_allele+1)/2); \
+            } \
             int nvals = dst->n_allele*(dst->n_allele+1)/2; \
             ENLARGE_ARRAY(type_t,set_missing,args->tmp_arr1,args->ntmp_arr1,1,nvals_ori,nvals); \
             vals = (type_t*) args->tmp_arr1; \
@@ -1139,8 +863,10 @@ static void merge_info_numeric(args_t *args, bcf1_t **lines, int nlines, bcf_inf
             { \
                 int ntmp2 = args->ntmp_arr2 / sizeof(type_t); \
                 int nvals2 = bcf_get_info_##type(args->hdr,lines[i],tag,&args->tmp_arr2,&ntmp2); \
+                if (nvals2<0) continue; /* info tag does not exist in this record, skip */ \
                 args->ntmp_arr2 = ntmp2 * sizeof(type_t); \
-                assert( nvals2==lines[i]->n_allele*(lines[i]->n_allele+1)/2 ); \
+                if (nvals2!=lines[i]->n_allele*(lines[i]->n_allele+1)/2) \
+                    error("vcfnorm: could not merge INFO tag %s at position %s:%d\n", tag, bcf_seqname(args->hdr,lines[i]),lines[i]->pos+1); \
                 vals2 = (type_t*) args->tmp_arr2; \
                 int ia,ib; \
                 k = 0; \
@@ -1192,6 +918,7 @@ static void merge_info_string(args_t *args, bcf1_t **lines, int nlines, bcf_info
         for (i=0; i<nlines; i++)
         {
             bcf_info_t *src = bcf_get_info(args->hdr,lines[i],tag);
+            if (!src) continue;
             for (j=jfrom; j<lines[i]->n_allele; j++)
                 copy_string_field((char*)src->vptr, j-jfrom, src->len, &str, args->maps[i].map[j]-jfrom);
         }
@@ -1208,6 +935,7 @@ static void merge_info_string(args_t *args, bcf1_t **lines, int nlines, bcf_info
         for (i=0; i<nlines; i++)
         {
             bcf_info_t *src = bcf_get_info(args->hdr,lines[i],tag);
+            if (!src) continue;
             int iori, jori, kori = 0;
             for (iori=0; iori<lines[i]->n_allele; iori++)
             {
@@ -1231,7 +959,6 @@ static void merge_info_string(args_t *args, bcf1_t **lines, int nlines, bcf_info
         bcf_get_info_string(args->hdr,lines[0],tag,&args->tmp_arr1,&args->ntmp_arr1);
         bcf_update_info_string(args->hdr,dst,tag,args->tmp_arr1);
     }
-
 }
 static void merge_format_genotype(args_t *args, bcf1_t **lines, int nlines, bcf_fmt_t *fmt, bcf1_t *dst)
 {
@@ -1250,7 +977,7 @@ static void merge_format_genotype(args_t *args, bcf1_t **lines, int nlines, bcf_
         int ngts2 = bcf_get_genotypes(args->hdr,lines[i],&args->tmp_arr2,&ntmp2);
         args->ntmp_arr2 = ntmp2 * 4;
         ngts2 /= nsmpl;
-        assert( ngts==ngts2 );
+        if ( ngts!=ngts2 ) error("Error at %s:%d: cannot combine diploid with haploid genotype\n", bcf_seqname(args->hdr,lines[i]),lines[i]->pos+1);
 
         int32_t *gt  = (int32_t*) args->tmp_arr1;
         int32_t *gt2 = (int32_t*) args->tmp_arr2;
@@ -1274,9 +1001,21 @@ static void merge_format_genotype(args_t *args, bcf1_t **lines, int nlines, bcf_
     }
     bcf_update_genotypes(args->hdr,dst,args->tmp_arr1,ngts*nsmpl);
 }
+static int diploid_to_haploid(int size, int nsmpl, int nals, uint8_t *vals)
+{
+    int i, dsrc = size*nals*(nals+1)/2, ddst = size*nals;
+    uint8_t *src_ptr = vals + dsrc, *dst_ptr = vals + ddst;
+    for (i=1; i<nsmpl; i++)
+    {
+        memmove(dst_ptr,src_ptr,ddst);
+        dst_ptr += ddst;
+        src_ptr += dsrc;
+    }
+    return nals;
+}
 static void merge_format_numeric(args_t *args, bcf1_t **lines, int nlines, bcf_fmt_t *fmt, bcf1_t *dst)
 {
-    #define BRANCH_NUMERIC(type,type_t,set_missing,is_vector_end) \
+    #define BRANCH_NUMERIC(type,type_t,set_missing,is_vector_end,set_vector_end) \
     { \
         const char *tag = bcf_hdr_int2id(args->hdr,BCF_DT_ID,fmt->id); \
         int ntmp = args->ntmp_arr1 / sizeof(type_t); \
@@ -1295,9 +1034,11 @@ static void merge_format_numeric(args_t *args, bcf1_t **lines, int nlines, bcf_f
             { \
                 int ntmp2 = args->ntmp_arr2 / sizeof(type_t); \
                 int nvals2 = bcf_get_format_##type(args->hdr,lines[i],tag,&args->tmp_arr2,&ntmp2); \
+                if (nvals2<0) continue; /* format tag does not exist in this record, skip */ \
                 args->ntmp_arr2 = ntmp2 * sizeof(type_t); \
                 nvals2 /= nsmpl; \
-                assert( nvals2==lines[i]->n_allele-1 ); \
+                if (nvals2!=lines[i]->n_allele-1) \
+                    error("vcfnorm: could not merge FORMAT tag %s at position %s:%d\n", tag, bcf_seqname(args->hdr,lines[i]),lines[i]->pos+1); \
                 vals  = (type_t*) args->tmp_arr1; \
                 vals2 = (type_t*) args->tmp_arr2; \
                 for (j=0; j<nsmpl; j++) \
@@ -1321,9 +1062,11 @@ static void merge_format_numeric(args_t *args, bcf1_t **lines, int nlines, bcf_f
             { \
                 int ntmp2 = args->ntmp_arr2 / sizeof(type_t); \
                 int nvals2 = bcf_get_format_##type(args->hdr,lines[i],tag,&args->tmp_arr2,&ntmp2); \
+                if (nvals2<0) continue; /* format tag does not exist in this record, skip */ \
                 args->ntmp_arr2 = ntmp2 * sizeof(type_t); \
                 nvals2 /= nsmpl; \
-                assert( nvals2==lines[i]->n_allele ); \
+                if (nvals2!=lines[i]->n_allele) \
+                    error("vcfnorm: could not merge FORMAT tag %s at position %s:%d\n", tag, bcf_seqname(args->hdr,lines[i]),lines[i]->pos+1); \
                 vals  = (type_t*) args->tmp_arr1; \
                 vals2 = (type_t*) args->tmp_arr2; \
                 for (j=0; j<nsmpl; j++) \
@@ -1341,33 +1084,50 @@ static void merge_format_numeric(args_t *args, bcf1_t **lines, int nlines, bcf_f
         } \
         else if ( len==BCF_VL_G ) \
         { \
-            int all_haploid = nvals_ori==lines[0]->n_allele ? 1 : 0; \
-            int nvals = all_haploid ? dst->n_allele : dst->n_allele*(dst->n_allele+1)/2; \
+            /* which samples are diploid */ \
+            memset(args->diploid,0,nsmpl); \
+            int all_haploid = 1; \
+            if ( nvals_ori > lines[0]->n_allele ) /* line possibly diploid */ \
+            { \
+                vals2 = (type_t*) args->tmp_arr1; \
+                int ndiploid = lines[0]->n_allele*(lines[0]->n_allele+1)/2; \
+                for (i=0; i<nsmpl; i++) \
+                { \
+                    if ( !args->diploid[i] ) \
+                    { \
+                        for (k=0; k<nvals_ori; k++) if ( is_vector_end ) break; \
+                        if ( k==ndiploid ) { args->diploid[i] = 1; all_haploid = 0; }\
+                    } \
+                    vals2 += nvals_ori; \
+                } \
+            } \
+            int nvals = dst->n_allele*(dst->n_allele+1)/2; \
             ENLARGE_ARRAY(type_t,set_missing,args->tmp_arr1,args->ntmp_arr1,nsmpl,nvals_ori,nvals); \
             for (i=1; i<nlines; i++) \
             { \
                 int ntmp2 = args->ntmp_arr2 / sizeof(type_t); \
                 int nvals2 = bcf_get_format_##type(args->hdr,lines[i],tag,&args->tmp_arr2,&ntmp2); \
+                if (nvals2<0) continue; /* format tag does not exist in this record, skip */ \
                 args->ntmp_arr2 = ntmp2 * sizeof(type_t); \
                 nvals2 /= nsmpl; \
-                assert( nvals2==lines[i]->n_allele || nvals2==lines[i]->n_allele*(lines[i]->n_allele+1)/2); \
+                int ndiploid = lines[i]->n_allele*(lines[i]->n_allele+1)/2; \
+                int line_diploid = nvals2==ndiploid ? 1 : 0; \
+                if (!(nvals2==1 || nvals2==lines[i]->n_allele || nvals2==lines[i]->n_allele*(lines[i]->n_allele+1)/2)) \
+                    error("vcfnorm: could not merge FORMAT tag %s at position %s:%d\n", tag, bcf_seqname(args->hdr,lines[i]),lines[i]->pos+1); \
                 vals  = (type_t*) args->tmp_arr1; \
                 vals2 = (type_t*) args->tmp_arr2; \
                 for (j=0; j<nsmpl; j++) \
                 { \
-                    int haploid = all_haploid; \
-                    if ( !haploid ) \
+                    int smpl_diploid = line_diploid; \
+                    if ( smpl_diploid ) \
                     { \
                         for (k=0; k<nvals2; k++) if ( is_vector_end ) break; \
-                        if ( k!=nvals2 ) haploid = 1; \
+                        if ( k!=ndiploid ) smpl_diploid = 0; \
                     } \
-                    if ( haploid ) \
+                    if ( smpl_diploid && !args->diploid[j] ) { args->diploid[j] = 1; all_haploid = 0; } \
+                    if ( !smpl_diploid ) \
                     { \
-                        for (k=0; k<nvals2; k++) \
-                        { \
-                            if ( is_vector_end ) break; \
-                            vals[ args->maps[i].map[k] ] = vals2[k]; \
-                        } \
+                        for (k=0; k<lines[i]->n_allele; k++) vals[args->maps[i].map[k]] = vals2[k]; \
                     } \
                     else \
                     { \
@@ -1387,6 +1147,18 @@ static void merge_format_numeric(args_t *args, bcf1_t **lines, int nlines, bcf_f
                     vals2 += nvals2; \
                 } \
             } \
+            if ( all_haploid ) \
+                nvals = diploid_to_haploid(sizeof(type_t),nsmpl,dst->n_allele,args->tmp_arr1); \
+            else \
+            {\
+                k = dst->n_allele;\
+                vals2 = (type_t*) args->tmp_arr1;\
+                for (i=0; i<nsmpl; i++)\
+                {\
+                    if ( !args->diploid[i] ) set_vector_end;\
+                    vals2 += nvals;\
+                }\
+            }\
             bcf_update_format_##type(args->hdr,dst,tag,args->tmp_arr1,nvals*nsmpl); \
         } \
         else \
@@ -1394,8 +1166,8 @@ static void merge_format_numeric(args_t *args, bcf1_t **lines, int nlines, bcf_f
     }
     switch (bcf_hdr_id2type(args->hdr,BCF_HL_FMT,fmt->id))
     {
-        case BCF_HT_INT:  BRANCH_NUMERIC(int32, int32_t, dst_ptr[k]=bcf_int32_missing, vals2[k]==bcf_int32_vector_end); break;
-        case BCF_HT_REAL: BRANCH_NUMERIC(float, float, bcf_float_set_missing(dst_ptr[k]), bcf_float_is_vector_end(vals2[k])); break;
+        case BCF_HT_INT:  BRANCH_NUMERIC(int32, int32_t, dst_ptr[k]=bcf_int32_missing, vals2[k]==bcf_int32_vector_end, vals2[k]=bcf_int32_vector_end); break;
+        case BCF_HT_REAL: BRANCH_NUMERIC(float, float, bcf_float_set_missing(dst_ptr[k]), bcf_float_is_vector_end(vals2[k]), bcf_float_set_vector_end(vals2[k])); break;
     }
     #undef BRANCH_NUMERIC
 }
@@ -1426,6 +1198,7 @@ static void merge_format_string(args_t *args, bcf1_t **lines, int nlines, bcf_fm
         for (i=0; i<nlines; i++)
         {
             int nret = bcf_get_format_char(args->hdr,lines[i],tag,&args->tmp_arr1,&args->ntmp_arr1);
+            if (nret<0) continue; /* format tag does not exist in this record, skip */ \
             nret /= nsmpl;
             for (k=0; k<nsmpl; k++)
             {
@@ -1472,6 +1245,7 @@ static void merge_format_string(args_t *args, bcf1_t **lines, int nlines, bcf_fm
             if ( i ) // we already have a copy
             {
                 nret = bcf_get_format_char(args->hdr,lines[i],tag,&args->tmp_arr1,&args->ntmp_arr1);
+                if (nret<0) continue; /* format tag does not exist in this record, skip */ \
                 nret /= nsmpl;
             }
             for (k=0; k<nsmpl; k++)
@@ -1552,22 +1326,18 @@ static void merge_biallelics_to_multiallelic(args_t *args, bcf1_t *dst, bcf1_t *
     }
     for (i=1; i<nlines; i++)
     {
-        if (lines[i]->d.id[0]!='.' || lines[i]->d.id[1]) {
-            kstring_t tmp = {0,0,0};
-            if (dst->d.id[0]=='.' && !dst->d.id[1])
-                kputs(lines[i]->d.id, &tmp);
-            else
-                ksprintf(&tmp, "%s;%s", dst->d.id, lines[i]->d.id);
-            bcf_update_id(args->hdr, dst, tmp.s);
-            free(tmp.s);
-        }
+        if (lines[i]->d.id[0]!='.' || lines[i]->d.id[1]) bcf_add_id(args->hdr, dst, lines[i]->d.id);
         args->maps[i].nals = lines[i]->n_allele;
         hts_expand(int,args->maps[i].nals,args->maps[i].mals,args->maps[i].map);
         args->als = merge_alleles(lines[i]->d.allele, lines[i]->n_allele, args->maps[i].map, args->als, &args->nals, &args->mals);
         if ( !args->als ) error("Failed to merge alleles at %s:%d\n", bcf_seqname(args->hdr,dst),dst->pos+1);
     }
     bcf_update_alleles(args->hdr, dst, (const char**)args->als, args->nals);
-    for (i=0; i<args->nals; i++) free(args->als[i]);
+    for (i=0; i<args->nals; i++)
+    {
+        free(args->als[i]);
+        args->als[i] = NULL;
+    }
 
     if ( lines[0]->d.n_flt ) bcf_update_filter(args->hdr, dst, lines[0]->d.flt, lines[0]->d.n_flt);
     for (i=1; i<nlines; i++) {
@@ -1614,7 +1384,9 @@ static void merge_biallelics_to_multiallelic(args_t *args, bcf1_t *dst, bcf1_t *
 static void mrows_schedule(args_t *args, bcf1_t **line)
 {
     int i,m;
-    if ( args->mrows_collapse==COLLAPSE_ANY ||  bcf_get_variant_types(*line)&COLLAPSE_SNPS )
+    if ( args->mrows_collapse==COLLAPSE_ANY         // merge all record types together
+        || bcf_get_variant_types(*line)&VCF_SNP     // SNP, put into alines
+        || bcf_get_variant_types(*line)==VCF_REF )  // ref
     {
         args->nalines++;
         m = args->malines;
@@ -1639,6 +1411,17 @@ static int mrows_ready_to_flush(args_t *args, bcf1_t *line)
 }
 static bcf1_t *mrows_flush(args_t *args)
 {
+    if ( args->nblines && args->nalines==1 && bcf_get_variant_types(args->alines[0])==VCF_REF )
+    {
+        // By default, REF lines are merged with SNPs if SNPs and indels are to be kept separately.
+        // However, if there are indels only and a single REF line, merge it with indels.
+        args->nblines++;
+        int i,m = args->mblines;
+        hts_expand(bcf1_t*,args->nblines,args->mblines,args->blines);
+        for (i=m; i<args->mblines; i++) args->blines[i] = bcf_init1();
+        SWAP(bcf1_t*, args->blines[args->nblines-1], args->alines[0]);
+        args->nalines--;
+    }
     if ( args->nalines )
     {
         if ( args->nalines==1 )
@@ -1668,26 +1451,10 @@ static bcf1_t *mrows_flush(args_t *args)
 static void flush_buffer(args_t *args, htsFile *file, int n)
 {
     bcf1_t *line;
-    int i, k, prev_rid = -1, prev_pos = 0, prev_type = 0;
+    int i, k;
     for (i=0; i<n; i++)
     {
         k = rbuf_shift(&args->rbuf);
-        if ( args->mrows_op==MROWS_SPLIT )
-        {
-            int split = 1;
-            if ( args->mrows_collapse!=COLLAPSE_BOTH && args->mrows_collapse!=COLLAPSE_ANY )
-            {
-                if ( !(bcf_get_variant_types(args->lines[k]) & args->mrows_collapse) ) split = 0;
-            }
-            if ( split && args->lines[k]->n_allele>2 )
-            {
-                split_multiallelic_to_biallelics(args, args->lines[k]);
-                int j;
-                for (j=0; j<args->ntmp_lines; j++)
-                    bcf_write1(file, args->hdr, args->tmp_lines[j]);
-                continue;
-            }
-        }
         if ( args->mrows_op==MROWS_MERGE )
         {
             if ( mrows_ready_to_flush(args, args->lines[k]) )
@@ -1705,16 +1472,6 @@ static void flush_buffer(args_t *args, htsFile *file, int n)
                 continue;
             }
         }
-        // todo: merge with next record if POS and the type are same. For now, just discard if asked to do so.
-        if ( args->rmdup )
-        {
-            int line_type = bcf_get_variant_types(args->lines[k]);
-            if ( prev_rid>=0 && prev_rid==args->lines[k]->rid && prev_pos==args->lines[k]->pos && prev_type==line_type )
-                continue;
-            prev_rid  = args->lines[k]->rid;
-            prev_pos  = args->lines[k]->pos;
-            prev_type = line_type;
-        }
         bcf_write1(file, args->hdr, args->lines[k]);
     }
     if ( args->mrows_op==MROWS_MERGE && !args->rbuf.n )
@@ -1737,6 +1494,7 @@ static void init_data(args_t *args)
     {
         args->mrow_out = bcf_init1();
         args->tmp_str = (kstring_t*) calloc(bcf_hdr_nsamples(args->hdr),sizeof(kstring_t));
+        args->diploid = (uint8_t*) malloc(bcf_hdr_nsamples(args->hdr));
     }
 }
 
@@ -1747,12 +1505,12 @@ static void destroy_data(args_t *args)
         if ( args->lines[i] ) bcf_destroy1(args->lines[i]);
     free(args->lines);
     for (i=0; i<args->mtmp_lines; i++)
-        bcf_destroy1(args->tmp_lines[i]);
+        if ( args->tmp_lines[i] ) bcf_destroy1(args->tmp_lines[i]);
     free(args->tmp_lines);
-    for (i=0; i<args->nalines; i++)
+    for (i=0; i<args->malines; i++)
         bcf_destroy1(args->alines[i]);
     free(args->alines);
-    for (i=0; i<args->nblines; i++)
+    for (i=0; i<args->mblines; i++)
         bcf_destroy1(args->blines[i]);
     free(args->blines);
     for (i=0; i<args->mmaps; i++)
@@ -1770,50 +1528,113 @@ static void destroy_data(args_t *args)
     free(args->als);
     free(args->tmp_arr1);
     free(args->tmp_arr2);
+    free(args->diploid);
     if ( args->mrow_out ) bcf_destroy1(args->mrow_out);
     if ( args->fai ) fai_destroy(args->fai);
     if ( args->mseq ) free(args->seq);
-    if ( args->aln.nmat ) free(args->aln.mat);
-    if ( args->aln.m_arr ) { free(args->aln.ipos_arr); free(args->aln.lref_arr); free(args->aln.lseq_arr); }
 }
 
 
+static void normalize_line(args_t *args, bcf1_t **line_ptr)
+{
+    bcf1_t *line = *line_ptr;
+    if ( args->fai )
+    {
+        if ( args->check_ref & CHECK_REF_FIX ) fix_ref(args, line);
+        if ( args->do_indels )
+        {
+            int ret = realign(args, line);
+
+            // exclude broken VCF lines
+            if ( ret==ERR_REF_MISMATCH && args->check_ref & CHECK_REF_SKIP )
+            {
+                args->nskipped++;
+                return;
+            }
+            if ( ret==ERR_DUP_ALLELE )
+            {
+                if ( args->check_ref & CHECK_REF_FIX )
+                    fix_dup_alt(args, line);
+                else if ( args->check_ref==CHECK_REF_EXIT )
+                    error("Duplicate alleles at %s:%d; run with -cw to turn the error into warning or with -cs to fix.\n", bcf_seqname(args->hdr,line),line->pos+1);
+                else if ( args->check_ref & CHECK_REF_WARN )
+                    fprintf(stderr,"ALT_DUP\t%s\t%d\n", bcf_seqname(args->hdr,line),line->pos+1);
+            }
+        }
+    }
+
+    // insert into sorted buffer
+    rbuf_expand0(&args->rbuf,bcf1_t*,args->rbuf.n+1,args->lines);
+    int i,j;
+    i = j = rbuf_append(&args->rbuf);
+    if ( !args->lines[i] ) args->lines[i] = bcf_init1();
+    SWAP(bcf1_t*, (*line_ptr), args->lines[i]);
+    while ( rbuf_prev(&args->rbuf,&i) )
+    {
+        if ( args->lines[i]->pos > args->lines[j]->pos ) SWAP(bcf1_t*, args->lines[i], args->lines[j]);
+        j = i;
+    }
+}
+
 static void normalize_vcf(args_t *args)
 {
     htsFile *out = hts_open(args->output_fname, hts_bcf_wmode(args->output_type));
     if ( out == NULL ) error("Can't write to \"%s\": %s\n", args->output_fname, strerror(errno));
+    if ( args->n_threads ) hts_set_threads(out, args->n_threads);
     bcf_hdr_append_version(args->hdr, args->argc, args->argv, "bcftools_norm");
     bcf_hdr_write(out, args->hdr);
 
+    int prev_rid = -1, prev_pos = -1, prev_type = 0;
     while ( bcf_sr_next_line(args->files) )
     {
         args->ntotal++;
 
         bcf1_t *line = args->files->readers[0].buffer[0];
-        if ( args->fai )
+        if ( args->rmdup )
         {
-            if ( realign(args, line)<0 && args->check_ref & CHECK_REF_SKIP )
+            int line_type = bcf_get_variant_types(line);
+            if ( prev_rid>=0 && prev_rid==line->rid && prev_pos==line->pos )
             {
-                args->nskipped++;
-                continue;   // exclude broken VCF lines
+                if ( (args->rmdup>>1)&COLLAPSE_ANY ) continue;
+                if ( (args->rmdup>>1)&COLLAPSE_SNPS && line_type&(VCF_SNP|VCF_MNP) && prev_type&(VCF_SNP|VCF_MNP) ) continue;
+                if ( (args->rmdup>>1)&COLLAPSE_INDELS && line_type&(VCF_INDEL) && prev_type&(VCF_INDEL) ) continue;
+            }
+            else
+            {
+                prev_rid  = line->rid;
+                prev_pos  = line->pos;
+                prev_type = 0;
             }
+            prev_type |= line_type;
         }
 
         // still on the same chromosome?
-        int i, j, ilast = rbuf_last(&args->rbuf);
+        int i,j,ilast = rbuf_last(&args->rbuf);
         if ( ilast>=0 && line->rid != args->lines[ilast]->rid ) flush_buffer(args, out, args->rbuf.n); // new chromosome
 
-        // insert into sorted buffer
-        i = j = ilast = rbuf_append(&args->rbuf);
-        if ( !args->lines[i] ) args->lines[i] = bcf_init1();
-        SWAP(bcf1_t*, args->files->readers[0].buffer[0], args->lines[i]);
-        while ( rbuf_prev(&args->rbuf,&i) )
+        int split = 0;
+        if ( args->mrows_op==MROWS_SPLIT )
         {
-            if ( args->lines[i]->pos > args->lines[j]->pos ) SWAP(bcf1_t*, args->lines[i], args->lines[j]);
-            j = i;
+            split = 1;
+            if ( args->mrows_collapse!=COLLAPSE_BOTH && args->mrows_collapse!=COLLAPSE_ANY )
+            {
+                if ( !(bcf_get_variant_types(line) & args->mrows_collapse) ) split = 0;
+            }
+            if ( split && line->n_allele>2 )
+            {
+                args->nsplit++;
+                split_multiallelic_to_biallelics(args, line);
+                for (j=0; j<args->ntmp_lines; j++)
+                    normalize_line(args, &args->tmp_lines[j]);
+            }
+            else
+                split = 0;
         }
+        if ( !split )
+            normalize_line(args, &args->files->readers[0].buffer[0]);
 
         // find out how many sites to flush
+        ilast = rbuf_last(&args->rbuf);
         j = 0;
         for (i=-1; rbuf_next(&args->rbuf,&i); )
         {
@@ -1826,7 +1647,9 @@ static void normalize_vcf(args_t *args)
     flush_buffer(args, out, args->rbuf.n);
     hts_close(out);
 
-    fprintf(stderr,"Lines total/modified/skipped:\t%d/%d/%d\n", args->ntotal,args->nchanged,args->nskipped);
+    fprintf(stderr,"Lines   total/split/realigned/skipped:\t%d/%d/%d/%d\n", args->ntotal,args->nsplit,args->nchanged,args->nskipped);
+    if ( args->check_ref & CHECK_REF_FIX )
+        fprintf(stderr,"REF/ALT total/modified/added:  \t%d/%d/%d\n", args->nref.tot,args->nref.swap,args->nref.set);
 }
 
 static void usage(void)
@@ -1838,10 +1661,12 @@ static void usage(void)
     fprintf(stderr, "Usage:   bcftools norm [options] <in.vcf.gz>\n");
     fprintf(stderr, "\n");
     fprintf(stderr, "Options:\n");
-    fprintf(stderr, "    -c, --check-ref <e|w|x>           check REF alleles and exit (e), warn (w), exclude (x) bad sites [e]\n");
+    fprintf(stderr, "    -c, --check-ref <e|w|x|s>         check REF alleles and exit (e), warn (w), exclude (x), or set (s) bad sites [e]\n");
     fprintf(stderr, "    -D, --remove-duplicates           remove duplicate lines of the same type.\n");
+    fprintf(stderr, "    -d, --rm-dup <type>               remove duplicate snps|indels|both|any\n");
     fprintf(stderr, "    -f, --fasta-ref <file>            reference sequence\n");
     fprintf(stderr, "    -m, --multiallelics <-|+>[type]   split multiallelics (-) or join biallelics (+), type: snps|indels|both|any [both]\n");
+    fprintf(stderr, "    -N, --do-not-normalize            do not normalize indels (with -m or -c s)\n");
     fprintf(stderr, "    -o, --output <file>               write output to a file [standard output]\n");
     fprintf(stderr, "    -O, --output-type <type>          'b' compressed BCF; 'u' uncompressed BCF; 'z' compressed VCF; 'v' uncompressed VCF [v]\n");
     fprintf(stderr, "    -r, --regions <region>            restrict to comma-separated list of regions\n");
@@ -1850,6 +1675,7 @@ static void usage(void)
     fprintf(stderr, "    -t, --targets <region>            similar to -r but streams rather than index-jumps\n");
     fprintf(stderr, "    -T, --targets-file <file>         similar to -R but streams rather than index-jumps\n");
     fprintf(stderr, "    -w, --site-win <int>              buffer for sorting lines which changed position during realignment [1000]\n");
+    fprintf(stderr, "        --threads <int>               number of extra output compression threads [0]\n");
     fprintf(stderr, "\n");
     exit(1);
 }
@@ -1862,32 +1688,45 @@ int main_vcfnorm(int argc, char *argv[])
     args->files   = bcf_sr_init();
     args->output_fname = "-";
     args->output_type = FT_VCF;
+    args->n_threads = 0;
     args->aln_win = 100;
     args->buf_win = 1000;
     args->mrows_collapse = COLLAPSE_BOTH;
+    args->do_indels = 1;
     int region_is_file  = 0;
     int targets_is_file = 0;
 
     static struct option loptions[] =
     {
-        {"help",0,0,'h'},
-        {"fasta-ref",1,0,'f'},
-        {"multiallelics",1,0,'m'},
-        {"regions",1,0,'r'},
-        {"regions-file",1,0,'R'},
-        {"targets",1,0,'t'},
-        {"targets-file",1,0,'T'},
-        {"site-win",1,0,'W'},
-        {"remove-duplicates",0,0,'D'},
-        {"output",1,0,'o'},
-        {"output-type",1,0,'O'},
-        {"check-ref",1,0,'c'},
-        {"strict-filter",0,0,'s'},
-        {0,0,0,0}
+        {"help",no_argument,NULL,'h'},
+        {"fasta-ref",required_argument,NULL,'f'},
+        {"do-not-normalize",no_argument,NULL,'N'},
+        {"multiallelics",required_argument,NULL,'m'},
+        {"regions",required_argument,NULL,'r'},
+        {"regions-file",required_argument,NULL,'R'},
+        {"targets",required_argument,NULL,'t'},
+        {"targets-file",required_argument,NULL,'T'},
+        {"site-win",required_argument,NULL,'w'},
+        {"remove-duplicates",no_argument,NULL,'D'},
+        {"rm-dup",required_argument,NULL,'d'},
+        {"output",required_argument,NULL,'o'},
+        {"output-type",required_argument,NULL,'O'},
+        {"threads",required_argument,NULL,9},
+        {"check-ref",required_argument,NULL,'c'},
+        {"strict-filter",no_argument,NULL,'s'},
+        {NULL,0,NULL,0}
     };
     char *tmp;
-    while ((c = getopt_long(argc, argv, "hr:R:f:w:Do:O:c:m:t:T:s",loptions,NULL)) >= 0) {
+    while ((c = getopt_long(argc, argv, "hr:R:f:w:Dd:o:O:c:m:t:T:sN",loptions,NULL)) >= 0) {
         switch (c) {
+            case 'N': args->do_indels = 0; break;
+            case 'd':
+                if ( !strcmp("snps",optarg) ) args->rmdup = COLLAPSE_SNPS<<1;
+                else if ( !strcmp("indels",optarg) ) args->rmdup = COLLAPSE_INDELS<<1;
+                else if ( !strcmp("both",optarg) ) args->rmdup = COLLAPSE_BOTH<<1;
+                else if ( !strcmp("any",optarg) ) args->rmdup = COLLAPSE_ANY<<1;
+                else error("The argument to -d not recognised: %s\n", optarg);
+                break;
             case 'm':
                 if ( optarg[0]=='-' ) args->mrows_op = MROWS_SPLIT;
                 else if ( optarg[0]=='+' ) args->mrows_op = MROWS_MERGE;
@@ -1904,6 +1743,7 @@ int main_vcfnorm(int argc, char *argv[])
             case 'c':
                 if ( strchr(optarg,'w') ) args->check_ref |= CHECK_REF_WARN;
                 if ( strchr(optarg,'x') ) args->check_ref |= CHECK_REF_SKIP;
+                if ( strchr(optarg,'s') ) args->check_ref |= CHECK_REF_FIX;
                 if ( strchr(optarg,'e') ) args->check_ref = CHECK_REF_EXIT; // overrides the above
                 break;
             case 'O':
@@ -1916,7 +1756,10 @@ int main_vcfnorm(int argc, char *argv[])
                 }
                 break;
             case 'o': args->output_fname = optarg; break;
-            case 'D': args->rmdup = 1; break;
+            case 'D':
+                fprintf(stderr,"Warning: `-D` is functional but deprecated, replaced by `-d both`.\n"); 
+                args->rmdup = COLLAPSE_NONE<<1;
+                break;
             case 's': args->strict_filter = 1; break;
             case 'f': args->ref_fname = optarg; break;
             case 'r': args->region = optarg; break;
@@ -1927,6 +1770,7 @@ int main_vcfnorm(int argc, char *argv[])
                 args->buf_win = strtol(optarg,&tmp,10);
                 if ( *tmp ) error("Could not parse argument: --site-win %s\n", optarg);
                 break;
+            case  9 : args->n_threads = strtol(optarg, 0, 0); break;
             case 'h':
             case '?': usage();
             default: error("Unknown argument: %s\n", optarg);
@@ -1934,6 +1778,7 @@ int main_vcfnorm(int argc, char *argv[])
     }
     if ( argc>optind+1 ) usage();
     if ( !args->ref_fname && !args->mrows_op && !args->rmdup ) usage();
+    if ( !args->ref_fname && args->check_ref&CHECK_REF_FIX ) error("Expected --fasta-ref with --check-ref s\n");
     char *fname = NULL;
     if ( optind>=argc )
     {
diff --git a/vcfplugin.c b/vcfplugin.c
index 9e2ee39..e2ca04a 100644
--- a/vcfplugin.c
+++ b/vcfplugin.c
@@ -1,6 +1,6 @@
-/*  vcfannotate.c -- Annotate and edit VCF/BCF files.
+/*  vcfplugin.c -- plugin modules for operating on VCF/BCF files.
 
-    Copyright (C) 2013-2014 Genome Research Ltd.
+    Copyright (C) 2013-2015 Genome Research Ltd.
 
     Author: Petr Danecek <pd3 at sanger.ac.uk>
 
@@ -129,7 +129,7 @@ typedef struct _args_t
     bcf_srs_t *files;
     bcf_hdr_t *hdr, *hdr_out;
     htsFile *out_fh;
-    int output_type;
+    int output_type, n_threads;
 
     filter_t *filter;
     char *filter_str;
@@ -146,30 +146,55 @@ args_t;
 
 char *msprintf(const char *fmt, ...);
 
-static void init_plugin_paths(args_t *args)
+static void add_plugin_paths(args_t *args, const char *path)
 {
-    if ( args->nplugin_paths!=-1 ) return;
-
-    char *path = getenv("BCFTOOLS_PLUGINS");
-    if ( path )
+    while (1)
     {
-        args->nplugin_paths = 1;
-        args->plugin_paths  = (char**) malloc(sizeof(char*));
-        char *ss = args->plugin_paths[0] = strdup(path);
-        while ( *ss )
+        size_t len = strcspn(path, ":");
+
+        if ( len == 0 )
+        {
+#ifdef PLUGINPATH
+            add_plugin_paths(args, PLUGINPATH);
+#endif
+        }
+        else
         {
-            if ( *ss==':' )
+            char *dir = (char *) malloc(len + 1);
+            strncpy(dir, path, len);
+            dir[len] = '\0';
+
+            struct stat st;
+            if ( stat(dir, &st) == 0 )
             {
-                *ss = 0;
                 args->plugin_paths = (char**) realloc(args->plugin_paths,sizeof(char*)*(args->nplugin_paths+1));
-                args->plugin_paths[args->nplugin_paths] = ss+1;
+                args->plugin_paths[args->nplugin_paths] = dir;
                 args->nplugin_paths++;
+                if ( args->verbose ) fprintf(stderr, "plugin directory %s .. ok\n", dir);
             }
-            ss++;
+            else
+            {
+                if ( args->verbose ) fprintf(stderr, "plugin directory %s .. %s\n", dir, strerror(errno));
+                free(dir);
+            }
+
         }
+
+        path += len;
+        if ( *path == ':' ) path++;
+        else break;
     }
-    else
-        args->nplugin_paths = 0;
+}
+
+static void init_plugin_paths(args_t *args)
+{
+    if ( args->nplugin_paths!=-1 ) return;
+
+    args->nplugin_paths = 0;
+    args->plugin_paths = NULL;
+
+    char *path = getenv("BCFTOOLS_PLUGINS");
+    add_plugin_paths(args, path ? path : "");
 }
 
 static void *dlopen_plugin(args_t *args, const char *fname)
@@ -247,7 +272,7 @@ static int load_plugin(args_t *args, const char *fname, int exit_on_error, plugi
     char *ret = dlerror();
     if ( ret )
         plugin->init = NULL;
-    else 
+    else
         if ( args->verbose ) fprintf(stderr,"\tinit     .. ok\n");
 
     plugin->run = (dl_run_f) dlsym(plugin->handle, "run");
@@ -398,6 +423,7 @@ static void init_data(args_t *args)
     {
         args->out_fh = hts_open(args->output_fname,hts_bcf_wmode(args->output_type));
         if ( args->out_fh == NULL ) error("Can't write to \"%s\": %s\n", args->output_fname, strerror(errno));
+        if ( args->n_threads ) hts_set_threads(args->out_fh, args->n_threads);
         bcf_hdr_write(args->out_fh, args->hdr_out);
     }
 }
@@ -410,7 +436,8 @@ static void destroy_data(args_t *args)
     if ( args->hdr_out ) bcf_hdr_destroy(args->hdr_out);
     if ( args->nplugin_paths>0 )
     {
-        free(args->plugin_paths[0]);
+        int i;
+        for (i=0; i<args->nplugin_paths; i++) free(args->plugin_paths[i]);
         free(args->plugin_paths);
     }
     if ( args->filter )
@@ -435,10 +462,12 @@ static void usage(args_t *args)
     fprintf(stderr, "VCF output options:\n");
     fprintf(stderr, "   -o, --output <file>         write output to a file [standard output]\n");
     fprintf(stderr, "   -O, --output-type <type>    'b' compressed BCF; 'u' uncompressed BCF; 'z' compressed VCF; 'v' uncompressed VCF [v]\n");
+    fprintf(stderr, "       --threads <int>         number of extra output compression threads [0]\n");
     fprintf(stderr, "Plugin options:\n");
     fprintf(stderr, "   -h, --help                  list plugin's options\n");
     fprintf(stderr, "   -l, --list-plugins          list available plugins. See BCFTOOLS_PLUGINS environment variable and man page for details\n");
     fprintf(stderr, "   -v, --verbose               print debugging information on plugin failure\n");
+    fprintf(stderr, "   -V, --version               print version string and exit\n");
     fprintf(stderr, "\n");
     exit(1);
 }
@@ -450,8 +479,9 @@ int main_plugin(int argc, char *argv[])
     args->argc    = argc; args->argv = argv;
     args->output_fname = "-";
     args->output_type = FT_VCF;
+    args->n_threads = 0;
     args->nplugin_paths = -1;
-    int regions_is_file = 0, targets_is_file = 0, plist_only = 0;
+    int regions_is_file = 0, targets_is_file = 0, plist_only = 0, usage_only = 0, version_only = 0;
 
     if ( argc==1 ) usage(args);
     char *plugin_name = NULL;
@@ -459,22 +489,25 @@ int main_plugin(int argc, char *argv[])
 
     static struct option loptions[] =
     {
-        {"verbose",0,0,'v'},
-        {"help",0,0,'h'},
-        {"list-plugins",0,0,'l'},
-        {"output",1,0,'o'},
-        {"output-type",1,0,'O'},
-        {"include",1,0,'i'},
-        {"exclude",1,0,'e'},
-        {"regions",1,0,'r'},
-        {"regions-file",1,0,'R'},
-        {"targets",1,0,'t'},
-        {"targets-file",1,0,'T'},
-        {0,0,0,0}
+        {"version",no_argument,NULL,'V'},
+        {"verbose",no_argument,NULL,'v'},
+        {"help",no_argument,NULL,'h'},
+        {"list-plugins",no_argument,NULL,'l'},
+        {"output",required_argument,NULL,'o'},
+        {"output-type",required_argument,NULL,'O'},
+        {"threads",required_argument,NULL,9},
+        {"include",required_argument,NULL,'i'},
+        {"exclude",required_argument,NULL,'e'},
+        {"regions",required_argument,NULL,'r'},
+        {"regions-file",required_argument,NULL,'R'},
+        {"targets",required_argument,NULL,'t'},
+        {"targets-file",required_argument,NULL,'T'},
+        {NULL,0,NULL,0}
     };
-    while ((c = getopt_long(argc, argv, "h?o:O:r:R:li:e:v",loptions,NULL)) >= 0)
+    while ((c = getopt_long(argc, argv, "h?o:O:r:R:t:T:li:e:vV",loptions,NULL)) >= 0)
     {
         switch (c) {
+            case 'V': version_only = 1; break;
             case 'v': args->verbose = 1; break;
             case 'o': args->output_fname = optarg; break;
             case 'O':
@@ -493,14 +526,34 @@ int main_plugin(int argc, char *argv[])
             case 't': args->targets_list = optarg; break;
             case 'T': args->targets_list = optarg; targets_is_file = 1; break;
             case 'l': plist_only = 1; break;
+            case  9 : args->n_threads = strtol(optarg, 0, 0); break;
             case '?':
-            case 'h': load_plugin(args, plugin_name, 1, &args->plugin); fprintf(stderr,"%s",args->plugin.usage()); return 0; break;
+            case 'h': usage_only = 1; break;
             default: error("Unknown argument: %s\n", optarg);
         }
     }
     if ( plist_only )  return list_plugins(args);
+    if ( usage_only && ! plugin_name ) usage(args);
 
     load_plugin(args, plugin_name, 1, &args->plugin);
+    if ( version_only )
+    {
+        const char *bver, *hver;
+        args->plugin.version(&bver, &hver);
+        printf("bcftools  %s using htslib %s\n", bcftools_version(), hts_version());
+        printf("plugin at %s using htslib %s\n\n", bver, hver);
+        return 0;
+    }
+
+    if ( usage_only )
+    {
+        if ( args->plugin.usage )
+            fprintf(stderr,"%s",args->plugin.usage());
+        else
+            fprintf(stderr,"Usage: bcftools +%s [General Options] -- [Plugin Options]\n",plugin_name);
+        return 0;
+    }
+
     if ( args->plugin.run )
     {
         int iopt = optind; optind = 0;
@@ -525,7 +578,6 @@ int main_plugin(int argc, char *argv[])
         args->plugin.argv = argv + optind;
     }
     optind = 0;
-    args->plugin.argv[0] = plugin_name;
 
     args->files = bcf_sr_init();
     if ( args->regions_list )
diff --git a/vcfquery.c b/vcfquery.c
index 7e72a1b..ab4c100 100644
--- a/vcfquery.c
+++ b/vcfquery.c
@@ -52,7 +52,7 @@ typedef struct
     bcf_hdr_t *header;
     int nsamples, *samples, sample_is_file;
     char **argv, *format_str, *sample_list, *targets_list, *regions_list, *vcf_list, *fn_out;
-    int argc, list_columns, print_header;
+    int argc, list_columns, print_header, allow_undef_tags;
     FILE *out;
 }
 args_t;
@@ -98,10 +98,16 @@ static void init_data(args_t *args)
         }
     }
     args->convert = convert_init(args->header, samples, nsamples, args->format_str);
+    if ( args->allow_undef_tags ) convert_set_option(args->convert, allow_undef_tags, 1);
     free(samples);
 
+    int max_unpack = convert_max_unpack(args->convert);
     if ( args->filter_str )
+    {
         args->filter = filter_init(args->header, args->filter_str);
+        max_unpack |= filter_max_unpack(args->filter);
+    }
+    args->files->max_unpack = max_unpack;
 }
 
 static void destroy_data(args_t *args)
@@ -188,6 +194,7 @@ static void usage(void)
     fprintf(stderr, "    -S, --samples-file <file>         file of samples to include\n");
     fprintf(stderr, "    -t, --targets <region>            similar to -r but streams rather than index-jumps\n");
     fprintf(stderr, "    -T, --targets-file <file>         similar to -R but streams rather than index-jumps\n");
+    fprintf(stderr, "    -u, --allow-undef-tags            print \".\" for undefined tags\n");
     fprintf(stderr, "    -v, --vcf-list <file>             process multiple VCFs listed in the file\n");
     fprintf(stderr, "\n");
     fprintf(stderr, "Examples:\n");
@@ -221,9 +228,10 @@ int main_vcfquery(int argc, char *argv[])
         {"print-header",0,0,'H'},
         {"collapse",1,0,'c'},
         {"vcf-list",1,0,'v'},
+        {"allow-undef-tags",0,0,'u'},
         {0,0,0,0}
     };
-    while ((c = getopt_long(argc, argv, "hlr:R:f:a:s:S:Ht:T:c:v:i:e:o:",loptions,NULL)) >= 0) {
+    while ((c = getopt_long(argc, argv, "hlr:R:f:a:s:S:Ht:T:c:v:i:e:o:u",loptions,NULL)) >= 0) {
         switch (c) {
             case 'o': args->fn_out = optarg; break;
             case 'f': args->format_str = strdup(optarg); break;
@@ -235,7 +243,7 @@ int main_vcfquery(int argc, char *argv[])
                 else if ( !strcmp(optarg,"both") ) collapse |= COLLAPSE_SNPS | COLLAPSE_INDELS;
                 else if ( !strcmp(optarg,"any") ) collapse |= COLLAPSE_ANY;
                 else if ( !strcmp(optarg,"all") ) collapse |= COLLAPSE_ANY;
-                else if ( !strcmp(optarg,"some") ) args->files->collapse |= COLLAPSE_SOME;
+                else if ( !strcmp(optarg,"some") ) collapse |= COLLAPSE_SOME;
                 else error("The --collapse string \"%s\" not recognised.\n", optarg);
                 break;
             case 'a':
@@ -262,6 +270,7 @@ int main_vcfquery(int argc, char *argv[])
             case 't': args->targets_list = optarg; break;
             case 'T': args->targets_list = optarg; targets_is_file = 1; break;
             case 'l': args->list_columns = 1; break;
+            case 'u': args->allow_undef_tags = 1; break;
             case 's': args->sample_list = optarg; break;
             case 'S': args->sample_list = optarg; args->sample_is_file = 1; break;
             case 'h':
diff --git a/vcfroh.c b/vcfroh.c
index 6ab2fc0..fa64b79 100644
--- a/vcfroh.c
+++ b/vcfroh.c
@@ -1,6 +1,6 @@
 /*  vcfroh.c -- HMM model for detecting runs of autozygosity.
 
-    Copyright (C) 2013-2014 Genome Research Ltd.
+    Copyright (C) 2013-2015 Genome Research Ltd.
 
     Author: Petr Danecek <pd3 at sanger.ac.uk>
 
@@ -49,7 +49,7 @@ typedef struct _args_t
     bcf_srs_t *files;
     bcf_hdr_t *hdr;
     double t2AZ, t2HW;      // P(AZ|HW) and P(HW|AZ) parameters
-    double unseen_PL;
+    double unseen_PL, dflt_AF;
 
     char *genmap_fname;
     genmap_t *genmap;
@@ -78,8 +78,8 @@ typedef struct _args_t
 }
 args_t;
 
-void set_tprob_genmap(hmm_t *hmm, uint32_t prev_pos, uint32_t pos, void *data);
-void set_tprob_recrate(hmm_t *hmm, uint32_t prev_pos, uint32_t pos, void *data);
+void set_tprob_genmap(hmm_t *hmm, uint32_t prev_pos, uint32_t pos, void *data, double *tprob);
+void set_tprob_recrate(hmm_t *hmm, uint32_t prev_pos, uint32_t pos, void *data, double *tprob);
 
 void *smalloc(size_t size)
 {
@@ -122,20 +122,21 @@ static void init_data(args_t *args)
         }
         free(smpls);
     }
-    else
+    else if ( !args->estimate_AF )
         kputs(args->sample, &str);
 
-    int ret = bcf_hdr_set_samples(args->hdr, str.s, 0);
-    if ( ret<0 ) error("Error parsing the list of samples: %s\n", str.s);
-    else if ( ret>0 ) error("The %d-th sample not found in the VCF\n", ret);
+    if ( str.l )
+    {
+        int ret = bcf_hdr_set_samples(args->hdr, str.s, 0);
+        if ( ret<0 ) error("Error parsing the list of samples: %s\n", str.s);
+        else if ( ret>0 ) error("The %d-th sample not found in the VCF\n", ret);
+    }
 
     if ( args->af_tag )
         if ( !bcf_hdr_idinfo_exists(args->hdr,BCF_HL_INFO,bcf_hdr_id2int(args->hdr,BCF_DT_ID,args->af_tag)) )
             error("No such INFO tag in the VCF: %s\n", args->af_tag);
 
-    if ( !bcf_sr_set_samples(args->files, str.s, 0) )
-        error("Error: could not set the samples %s\n", str.s);
-    args->nsmpl = args->files->n_smpl;
+    args->nsmpl = bcf_hdr_nsamples(args->hdr);
     args->ismpl = bcf_hdr_id2int(args->hdr, BCF_DT_SAMPLE, args->sample);
     free(str.s);
 
@@ -268,24 +269,24 @@ static double get_genmap_rate(args_t *args, int start, int end)
     return rate;
 }
 
-void set_tprob_genmap(hmm_t *hmm, uint32_t prev_pos, uint32_t pos, void *data)
+void set_tprob_genmap(hmm_t *hmm, uint32_t prev_pos, uint32_t pos, void *data, double *tprob)
 {
     args_t *args = (args_t*) data;
     double ci = get_genmap_rate(args, pos - prev_pos, pos);
-    MAT(hmm->curr_tprob,2,STATE_HW,STATE_HW) *= 1-ci;
-    MAT(hmm->curr_tprob,2,STATE_HW,STATE_AZ) *= ci;
-    MAT(hmm->curr_tprob,2,STATE_AZ,STATE_HW) *= ci;
-    MAT(hmm->curr_tprob,2,STATE_AZ,STATE_AZ) *= 1-ci;
+    MAT(tprob,2,STATE_HW,STATE_AZ) *= ci;
+    MAT(tprob,2,STATE_AZ,STATE_HW) *= ci;
+    MAT(tprob,2,STATE_AZ,STATE_AZ)  = 1 - MAT(tprob,2,STATE_HW,STATE_AZ);
+    MAT(tprob,2,STATE_HW,STATE_HW)  = 1 - MAT(tprob,2,STATE_AZ,STATE_HW);
 }
 
-void set_tprob_recrate(hmm_t *hmm, uint32_t prev_pos, uint32_t pos, void *data)
+void set_tprob_recrate(hmm_t *hmm, uint32_t prev_pos, uint32_t pos, void *data, double *tprob)
 {
     args_t *args = (args_t*) data;
     double ci = (pos - prev_pos) * args->rec_rate;
-    MAT(hmm->curr_tprob,2,STATE_HW,STATE_HW) *= 1-ci;
-    MAT(hmm->curr_tprob,2,STATE_HW,STATE_AZ) *= ci;
-    MAT(hmm->curr_tprob,2,STATE_AZ,STATE_HW) *= ci;
-    MAT(hmm->curr_tprob,2,STATE_AZ,STATE_AZ) *= 1-ci;
+    MAT(tprob,2,STATE_HW,STATE_AZ) *= ci;
+    MAT(tprob,2,STATE_AZ,STATE_HW) *= ci;
+    MAT(tprob,2,STATE_AZ,STATE_AZ)  = 1 - MAT(tprob,2,STATE_HW,STATE_AZ);
+    MAT(tprob,2,STATE_HW,STATE_HW)  = 1 - MAT(tprob,2,STATE_AZ,STATE_HW);
 }
 
 
@@ -301,19 +302,17 @@ void set_tprob_recrate(hmm_t *hmm, uint32_t prev_pos, uint32_t pos, void *data)
  *  Transition probabilities:
  *    tAZ = P(AZ|HW)  .. parameter
  *    tHW = P(HW|AZ)  .. parameter
- *    P(AZ|AZ) = 1 - P(HW|AZ) = 1 - tHW
- *    P(HW|HW) = 1 - P(AZ|HW) = 1 - tAZ
  *
  *    ci  = P_i(C)    .. probability of cross-over at site i, from genetic map
  *
  *    AZi = P_i(AZ)   .. probability of site i being AZ/non-AZ, scaled so that AZi+HWi = 1
  *    HWi = P_i(HW)
  *
- *    P_i(AZ|AZ) = P(AZ|AZ) * (1-ci) * AZ{i-1} = (1-tHW) * (1-ci) * AZ{i-1}
  *    P_i(AZ|HW) = P(AZ|HW) * ci * HW{i-1}     = tAZ * ci * (1 - AZ{i-1})
- *
- *    P_i(HW|HW) = P(HW|HW) * (1-ci) * HW{i-1} = (1-tAZ) * (1-ci) * (1 - AZ{i-1})
  *    P_i(HW|AZ) = P(HW|AZ) * ci * AZ{i-1}     = tHW * ci * AZ{i-1}
+ *    P_i(AZ|AZ) = 1 - P_i(HW|AZ)
+ *    P_i(HW|HW) = 1 - P_i(AZ|HW)
+ *
  */
 
 static void flush_viterbi(args_t *args)
@@ -326,11 +325,16 @@ static void flush_viterbi(args_t *args)
     {
         // single viterbi pass, one chromsome
         hmm_run_viterbi(args->hmm, args->nsites, args->eprob, args->sites);
+        hmm_run_fwd_bwd(args->hmm, args->nsites, args->eprob, args->sites);
+        double *fwd = hmm_get_fwd_bwd_prob(args->hmm);
 
         const char *chr = bcf_hdr_id2name(args->hdr,args->prev_rid);
+        uint8_t *vpath = hmm_get_viterbi_path(args->hmm);
         for (i=0; i<args->nsites; i++)
         {
-            printf("%s\t%d\t%d\t..\n", chr,args->sites[i]+1,args->hmm->vpath[i*2]==STATE_AZ ? 1 : 0);
+            int state = vpath[i*2]==STATE_AZ ? 1 : 0;
+            double *pval = fwd + i*2;
+            printf("%s\t%d\t%d\t%.1f\n", chr,args->sites[i]+1, state, phred_score(1.0-pval[state]));
         }
         return;
     }
@@ -341,8 +345,9 @@ static void flush_viterbi(args_t *args)
     int niter = 0;
     do
     {
-        t2az_prev = MAT(args->hmm->tprob_arr,2,1,0); //args->t2AZ;
-        t2hw_prev = MAT(args->hmm->tprob_arr,2,0,1); //args->t2HW;
+        double *tprob_arr = hmm_get_tprob(args->hmm);
+        t2az_prev = MAT(tprob_arr,2,1,0); //args->t2AZ;
+        t2hw_prev = MAT(tprob_arr,2,0,1); //args->t2HW;
         double tcounts[] = { 0,0,0,0 };
         for (i=0; i<args->nrids; i++)
         {
@@ -353,11 +358,12 @@ static void flush_viterbi(args_t *args)
             hmm_run_viterbi(args->hmm, nsites, args->eprob+ioff*2, args->sites+ioff);
 
             // what transitions were observed: add to the total counts
+            uint8_t *vpath = hmm_get_viterbi_path(args->hmm);
             for (j=1; j<nsites; j++)
             {
                 // count the number of transitions
-                int prev_state = args->hmm->vpath[2*(j-1)];
-                int curr_state = args->hmm->vpath[2*j];
+                int prev_state = vpath[2*(j-1)];
+                int curr_state = vpath[2*j];
                 MAT(tcounts,2,curr_state,prev_state) += 1;
             }
         }
@@ -367,7 +373,7 @@ static void flush_viterbi(args_t *args)
         {
             int n = 0;
             for (j=0; j<2; j++) n += MAT(tcounts,2,i,j);
-            error("fixme: state %d not observed\n", i+1);
+            if ( !n) error("fixme: state %d not observed\n", i+1);
             for (j=0; j<2; j++) MAT(tcounts,2,i,j) /= n;
         }
         if ( args->genmap_fname || args->rec_rate > 0 )
@@ -375,15 +381,17 @@ static void flush_viterbi(args_t *args)
         else
             hmm_set_tprob(args->hmm, tcounts, 10000);
 
-        deltaz = fabs(MAT(args->hmm->tprob_arr,2,1,0)-t2az_prev);
-        delthw = fabs(MAT(args->hmm->tprob_arr,2,0,1)-t2hw_prev);
+        tprob_arr = hmm_get_tprob(args->hmm);
+        deltaz = fabs(MAT(tprob_arr,2,1,0)-t2az_prev);
+        delthw = fabs(MAT(tprob_arr,2,0,1)-t2hw_prev);
         niter++;
 
         fprintf(stderr,"%d: %f %f\n", niter,deltaz,delthw);
     }
     while ( deltaz > 0.0 || delthw > 0.0 );
     fprintf(stderr, "Viterbi training converged in %d iterations to", niter);
-    for (i=0; i<2; i++) for (j=0; j<2; j++) fprintf(stderr, " %f", MAT(args->hmm->tprob_arr,2,i,j));
+    double *tprob_arr = hmm_get_tprob(args->hmm);
+    for (i=0; i<2; i++) for (j=0; j<2; j++) fprintf(stderr, " %f", MAT(tprob_arr,2,i,j));
     fprintf(stderr, "\n");
     
     // output the results
@@ -392,11 +400,12 @@ static void flush_viterbi(args_t *args)
         int ioff = args->rid_offs[i];
         int nsites = (i+1==args->nrids ? args->nsites : args->rid_offs[i+1]) - ioff;
         hmm_run_viterbi(args->hmm, nsites, args->eprob+ioff*2, args->sites+ioff);
+        uint8_t *vpath = hmm_get_viterbi_path(args->hmm);
 
         const char *chr = bcf_hdr_id2name(args->hdr,args->rids[i]);
         for (j=0; j<nsites; j++)
         {
-            printf("%s\t%d\t%d\t..\n", chr,args->sites[ioff+j]+1,args->hmm->vpath[j*2]==STATE_AZ ? 1 : 0);
+            printf("%s\t%d\t%d\t..\n", chr,args->sites[ioff+j]+1,vpath[j*2]==STATE_AZ ? 1 : 0);
         }
     }
 }
@@ -510,7 +519,11 @@ int parse_line(args_t *args, bcf1_t *line, double *alt_freq, double *pdg)
     }
 
     if ( ret<0 ) return ret;
-
+    if ( *alt_freq==0.0 )
+    {
+        if ( args->dflt_AF==0 ) return -1;       // we skip sites with AF=0
+        *alt_freq = args->dflt_AF;
+    }
 
     // Set P(D|G)
     if ( args->fake_PLs )
@@ -647,6 +660,7 @@ static void usage(args_t *args)
     fprintf(stderr, "Usage:   bcftools roh [options] <in.vcf.gz>\n");
     fprintf(stderr, "\n");
     fprintf(stderr, "General Options:\n");
+    fprintf(stderr, "        --AF-dflt <float>              if AF is not known, use this allele frequency [skip]\n");
     fprintf(stderr, "        --AF-tag <TAG>                 use TAG for allele frequency\n");
     fprintf(stderr, "        --AF-file <file>               read allele frequencies from file (CHR\\tPOS\\tREF,ALT\\tAF)\n");
     fprintf(stderr, "    -e, --estimate-AF <file>           calculate AC,AN counts on the fly, using either all samples (\"-\") or samples listed in <file>\n");
@@ -661,8 +675,8 @@ static void usage(args_t *args)
     fprintf(stderr, "    -T, --targets-file <file>          similar to -R but streams rather than index-jumps\n");
     fprintf(stderr, "\n");
     fprintf(stderr, "HMM Options:\n");
-    fprintf(stderr, "    -a, --hw-to-az <float>             P(AZ|HW) transition probability from AZ (autozygous) to HW (Hardy-Weinberg) state [1e-8]\n");
-    fprintf(stderr, "    -H, --az-to-hw <float>             P(HW|AZ) transition probability from HW to AZ state [1e-7]\n");
+    fprintf(stderr, "    -a, --hw-to-az <float>             P(AZ|HW) transition probability from HW (Hardy-Weinberg) to AZ (autozygous) state [6.7e-8]\n");
+    fprintf(stderr, "    -H, --az-to-hw <float>             P(HW|AZ) transition probability from AZ to HW state [5e-9]\n");
     fprintf(stderr, "    -V, --viterbi-training             perform Viterbi training to estimate transition probabilities\n");
     fprintf(stderr, "\n");
     exit(1);
@@ -674,8 +688,8 @@ int main_vcfroh(int argc, char *argv[])
     args_t *args  = (args_t*) calloc(1,sizeof(args_t));
     args->argc    = argc; args->argv = argv;
     args->files   = bcf_sr_init();
-    args->t2AZ    = 1e-1;
-    args->t2HW    = 1e-1;
+    args->t2AZ    = 6.7e-8;
+    args->t2HW    = 5e-9;
     args->rec_rate = 0;
     int regions_is_file = 0, targets_is_file = 0;
 
@@ -683,6 +697,7 @@ int main_vcfroh(int argc, char *argv[])
     {
         {"AF-tag",1,0,0},
         {"AF-file",1,0,1},
+        {"AF-dflt",1,0,2},
         {"estimate-AF",1,0,'e'},
         {"GTs-only",1,0,'G'},
         {"sample",1,0,'s'},
@@ -705,6 +720,10 @@ int main_vcfroh(int argc, char *argv[])
         switch (c) {
             case 0: args->af_tag = optarg; naf_opts++; break;
             case 1: args->af_fname = optarg; naf_opts++; break;
+            case 2: 
+                args->dflt_AF = strtod(optarg,&tmp);
+                if ( *tmp ) error("Could not parse: --AF-dflt %s\n", optarg);
+                break;
             case 'e': args->estimate_AF = optarg; naf_opts++; break;
             case 'I': args->snps_only = 1; break;
             case 'G':
diff --git a/vcfstats.c b/vcfstats.c
index a5caed4..1032bf8 100644
--- a/vcfstats.c
+++ b/vcfstats.c
@@ -1,6 +1,6 @@
 /*  vcfstats.c -- Produces stats which can be plotted using plot-vcfstats.
 
-    Copyright (C) 2012-2014 Genome Research Ltd.
+    Copyright (C) 2012-2015 Genome Research Ltd.
 
     Author: Petr Danecek <pd3 at sanger.ac.uk>
 
@@ -38,11 +38,17 @@ THE SOFTWARE.  */
 #include <htslib/faidx.h>
 #include <inttypes.h>
 #include "bcftools.h"
+#include "filter.h"
+
+// Logic of the filters: include or exclude sites which match the filters?
+#define FLT_INCLUDE 1
+#define FLT_EXCLUDE 2
 
 #define HWE_STATS 1
 #define QUAL_STATS 1
 #define IRC_STATS 1
 #define IRC_RLEN 10
+#define NA_STRING "0"
 
 typedef struct
 {
@@ -63,7 +69,18 @@ idist_t;
 
 typedef struct
 {
-    int n_snps, n_indels, n_mnps, n_others, n_mals, n_snp_mals, n_records;
+    double x;
+    double x2;
+    double y;
+    double y2;
+    double xy;
+    double n;
+}
+smpl_r_t;
+
+typedef struct
+{
+    int n_snps, n_indels, n_mnps, n_others, n_mals, n_snp_mals, n_records, n_noalts;
     int *af_ts, *af_tv, *af_snps;   // first bin of af_* stats are singletons
     #if HWE_STATS
         int *af_hwe;
@@ -80,6 +97,7 @@ typedef struct
     int in_frame, out_frame, na_frame, in_frame_alt1, out_frame_alt1, na_frame_alt1;
     int subst[15];
     int *smpl_hets, *smpl_homRR, *smpl_homAA, *smpl_ts, *smpl_tv, *smpl_indels, *smpl_ndp, *smpl_sngl;
+    int *smpl_indel_hets, *smpl_indel_homs;
     int *smpl_frm_shifts; // not-applicable, in-frame, out-frame
     unsigned long int *smpl_dp;
     idist_t dp, dp_sites;
@@ -133,6 +151,14 @@ typedef struct
     char **argv, *exons_fname, *regions_list, *samples_list, *targets_list;
     int argc, verbose_sites, first_allele_only, samples_is_file;
     int split_by_id, nstats;
+
+    filter_t *filter[2];
+    char *filter_str;
+    int filter_logic;   // include or exclude sites which match the filters? One of FLT_INCLUDE/FLT_EXCLUDE
+
+    // Per Sample r working data arrays of size equal to number of samples
+    smpl_r_t* smpl_r_snps;
+    smpl_r_t* smpl_r_indels;
 }
 args_t;
 
@@ -372,6 +398,13 @@ static void init_stats(args_t *args)
     args->nstats = args->files->nreaders==1 ? 1 : 3;
     if ( args->split_by_id ) args->nstats = 2;
 
+    if ( args->filter_str )
+    {
+        args->filter[0] = filter_init(bcf_sr_get_header(args->files,0), args->filter_str);
+        if ( args->files->nreaders==2 )
+            args->filter[1] = filter_init(bcf_sr_get_header(args->files,1), args->filter_str);
+    }
+
     // AF corresponds to AC but is more robust for mixture of haploid and diploid GTs
     args->m_af = 101;
     for (i=0; i<args->files->nreaders; i++)
@@ -397,6 +430,8 @@ static void init_stats(args_t *args)
         args->af_gts_indels   = (gtcmp_t *) calloc(args->m_af,sizeof(gtcmp_t));
         args->smpl_gts_snps   = (gtcmp_t *) calloc(args->files->n_smpl,sizeof(gtcmp_t));
         args->smpl_gts_indels = (gtcmp_t *) calloc(args->files->n_smpl,sizeof(gtcmp_t));
+        args->smpl_r_snps = (smpl_r_t*) calloc(args->files->n_smpl, sizeof(smpl_r_t));
+        args->smpl_r_indels = (smpl_r_t*) calloc(args->files->n_smpl, sizeof(smpl_r_t));
     }
     for (i=0; i<args->nstats; i++)
     {
@@ -420,6 +455,8 @@ static void init_stats(args_t *args)
             stats->smpl_hets   = (int *) calloc(args->files->n_smpl,sizeof(int));
             stats->smpl_homAA  = (int *) calloc(args->files->n_smpl,sizeof(int));
             stats->smpl_homRR  = (int *) calloc(args->files->n_smpl,sizeof(int));
+            stats->smpl_indel_hets = (int *) calloc(args->files->n_smpl,sizeof(int));
+            stats->smpl_indel_homs = (int *) calloc(args->files->n_smpl,sizeof(int));
             stats->smpl_ts     = (int *) calloc(args->files->n_smpl,sizeof(int));
             stats->smpl_tv     = (int *) calloc(args->files->n_smpl,sizeof(int));
             stats->smpl_indels = (int *) calloc(args->files->n_smpl,sizeof(int));
@@ -497,6 +534,8 @@ static void destroy_stats(args_t *args)
         if (stats->smpl_hets) free(stats->smpl_hets);
         if (stats->smpl_homAA) free(stats->smpl_homAA);
         if (stats->smpl_homRR) free(stats->smpl_homRR);
+        if (stats->smpl_indel_homs) free(stats->smpl_indel_homs);
+        if (stats->smpl_indel_hets) free(stats->smpl_indel_hets);
         if (stats->smpl_ts) free(stats->smpl_ts);
         if (stats->smpl_tv) free(stats->smpl_tv);
         if (stats->smpl_indels) free(stats->smpl_indels);
@@ -517,13 +556,17 @@ static void destroy_stats(args_t *args)
     for (j=0; j<args->nusr; j++) free(args->usr[j].tag);
     free(args->usr);
     free(args->tmp_frm);
-    if (args->tmp_iaf) free(args->tmp_iaf);
+    free(args->tmp_iaf);
     if (args->exons) bcf_sr_regions_destroy(args->exons);
-    if (args->af_gts_snps) free(args->af_gts_snps);
-    if (args->af_gts_indels) free(args->af_gts_indels);
-    if (args->smpl_gts_snps) free(args->smpl_gts_snps);
-    if (args->smpl_gts_indels) free(args->smpl_gts_indels);
+    free(args->af_gts_snps);
+    free(args->af_gts_indels);
+    free(args->smpl_gts_snps);
+    free(args->smpl_gts_indels);
+    free(args->smpl_r_snps);
+    free(args->smpl_r_indels);
     if (args->indel_ctx) indel_ctx_destroy(args->indel_ctx);
+    if (args->filter[0]) filter_destroy(args->filter[0]);
+    if (args->filter[1]) filter_destroy(args->filter[1]);
 }
 
 static void init_iaf(args_t *args, bcf_sr_t *reader)
@@ -790,7 +833,7 @@ static void do_sample_stats(args_t *args, stats_t *stats, bcf_sr_t *reader, int
                     case GT_HOM_AA: nalt_tot++; break;
                 }
             #endif
-            if ( line_type&VCF_SNP )
+            if ( line_type&VCF_SNP || line_type==VCF_REF )  // count ALT=. as SNP
             {
                 if ( gt == GT_HET_RA ) stats->smpl_hets[is]++;
                 else if ( gt == GT_HET_AA ) stats->smpl_hets[is]++;
@@ -808,7 +851,12 @@ static void do_sample_stats(args_t *args, stats_t *stats, bcf_sr_t *reader, int
             }
             if ( line_type&VCF_INDEL )
             {
-                if ( gt != GT_HOM_RR ) stats->smpl_indels[is]++;
+                if ( gt != GT_HOM_RR )
+                {
+                    stats->smpl_indels[is]++;
+                    if ( gt==GT_HET_RA || gt==GT_HET_AA ) stats->smpl_indel_hets[is]++;
+                    else if ( gt==GT_HOM_AA ) stats->smpl_indel_homs[is]++;
+                }
                 if ( stats->smpl_frm_shifts )
                 {
                     assert( ial<line->n_allele && jal<line->n_allele );
@@ -868,8 +916,28 @@ static void do_sample_stats(args_t *args, stats_t *stats, bcf_sr_t *reader, int
         gtcmp_t *af_stats = line_type&VCF_SNP ? args->af_gts_snps : args->af_gts_indels;
         gtcmp_t *smpl_stats = line_type&VCF_SNP ? args->smpl_gts_snps : args->smpl_gts_indels;
 
+        //
+        // Calculates r squared
+        // x is mean dosage of x at given site
+        // x2 is mean squared dosage of x at given site
+        // y is mean dosage of x at given site
+        // y2 is mean squared dosage of x at given site
+        // xy is mean dosage of x*y at given site
+        // r2sum += (xy - x*y)^2 / ( (x2 - x^2) * (y2 - y^2) )
+        // r2n is number of sites considered
+        // output as r2sum/r2n for each AF bin
         int r2n = 0;
         float x = 0, y = 0, xy = 0, x2 = 0, y2 = 0;
+        // Select smpl_r
+        smpl_r_t *smpl_r = NULL;
+        if (line_type&VCF_SNP)
+        {
+            smpl_r = args->smpl_r_snps;
+        }
+        else if (line_type&VCF_INDEL)
+        {
+            smpl_r = args->smpl_r_indels;
+        }
         for (is=0; is<files->n_smpl; is++)
         {
             // Simplified comparison: only 0/0, 0/1, 1/1 is looked at as the identity of
@@ -903,7 +971,18 @@ static void do_sample_stats(args_t *args, stats_t *stats, bcf_sr_t *reader, int
                 smpl_stats[is].mm[idx]++;
             }
 
+            // Now do it across samples
+
+            if (smpl_r) {
+                smpl_r[is].xy += dsg0*dsg1;
+                smpl_r[is].x += dsg0;
+                smpl_r[is].x2 += dsg0*dsg0;
+                smpl_r[is].y += dsg1;
+                smpl_r[is].y2 += dsg1*dsg1;
+                ++(smpl_r[is].n);
+            }
         }
+
         if ( r2n )
         {
             x /= r2n; y /= r2n; x2 /= r2n; y2 /= r2n; xy /= r2n;
@@ -951,15 +1030,26 @@ static void do_vcf_stats(args_t *args)
     {
         bcf_sr_t *reader = NULL;
         bcf1_t *line = NULL;
-        int ret = 0, i;
+        int ret = 0, i, pass = 1;
         for (i=0; i<files->nreaders; i++)
         {
             if ( !bcf_sr_has_line(files,i) ) continue;
+            if ( args->filter[i] )
+            {
+                int is_ok = filter_test(args->filter[i], bcf_sr_get_line(files,i), NULL);
+                if ( args->filter_logic & FLT_EXCLUDE ) is_ok = is_ok ? 0 : 1;
+                if ( !is_ok ) { pass = 0; break; }
+            }
             ret |= 1<<i;
-            if ( reader ) continue;
-            reader = &files->readers[i];
-            line = files->readers[i].buffer[0];
+            if ( !reader )
+            {
+                reader = &files->readers[i];
+                line = bcf_sr_get_line(files,i);
+            }
+
         }
+        if ( !pass ) continue;
+
         int line_type = bcf_get_variant_types(line);
         init_iaf(args, reader);
 
@@ -969,6 +1059,8 @@ static void do_vcf_stats(args_t *args)
 
         stats->n_records++;
 
+        if ( line_type==VCF_REF )
+            stats->n_noalts++;
         if ( line_type&VCF_SNP )
             do_snp_stats(args, stats, reader);
         if ( line_type&VCF_INDEL )
@@ -1045,6 +1137,7 @@ static void print_stats(args_t *args)
     {
         stats_t *stats = &args->stats[id];
         printf("SN\t%d\tnumber of records:\t%d\n", id, stats->n_records);
+        printf("SN\t%d\tnumber of no-ALTs:\t%d\n", id, stats->n_noalts);
         printf("SN\t%d\tnumber of SNPs:\t%d\n", id, stats->n_snps);
         printf("SN\t%d\tnumber of MNPs:\t%d\n", id, stats->n_mnps);
         printf("SN\t%d\tnumber of indels:\t%d\n", id, stats->n_indels);
@@ -1229,23 +1322,37 @@ static void print_stats(args_t *args)
         for (x=0; x<2; x++)
         {
             gtcmp_t *stats;
+            smpl_r_t *smpl_r_array;
             if ( x==0 )
             {
-                printf("# GCcS, Genotype concordance by sample (SNPs)\n# GCsS\t[2]id\t[3]sample\t[4]non-reference discordance rate\t[5]RR Hom matches\t[6]RA Het matches\t[7]AA Hom matches\t[8]RR Hom mismatches\t[9]RA Het mismatches\t[10]AA Hom mismatches\n");
+                printf("# GCsS, Genotype concordance by sample (SNPs)\n# GCsS\t[2]id\t[3]sample\t[4]non-reference discordance rate\t[5]RR Hom matches\t[6]RA Het matches\t[7]AA Hom matches\t[8]RR Hom mismatches\t[9]RA Het mismatches\t[10]AA Hom mismatches\t[11]dosage r-squared\n");
                 stats = args->smpl_gts_snps;
+                smpl_r_array = args->smpl_r_snps;
             }
             else
             {
-                printf("# GCiS, Genotype concordance by sample (indels)\n# GCiS\t[2]id\t[3]sample\t[4]non-reference discordance rate\t[5]RR Hom matches\t[6]RA Het matches\t[7]AA Hom matches\t[8]RR Hom mismatches\t[9]RA Het mismatches\t[10]AA Hom mismatches\n");
+                printf("# GCiS, Genotype concordance by sample (indels)\n# GCiS\t[2]id\t[3]sample\t[4]non-reference discordance rate\t[5]RR Hom matches\t[6]RA Het matches\t[7]AA Hom matches\t[8]RR Hom mismatches\t[9]RA Het mismatches\t[10]AA Hom mismatches\t[11]dosage r-squared\n");
                 stats = args->smpl_gts_indels;
+                smpl_r_array = args->smpl_r_indels;
             }
             for (i=0; i<args->files->n_smpl; i++)
             {
                 uint64_t m  = stats[i].m[T2S(GT_HET_RA)] + stats[i].m[T2S(GT_HOM_AA)];
                 uint64_t mm = stats[i].mm[T2S(GT_HOM_RR)] + stats[i].mm[T2S(GT_HET_RA)] + stats[i].mm[T2S(GT_HOM_AA)];
+                // Calculate r by formula 19.2 - Biostatistical Analysis 4th edition - Jerrold H. Zar
+                smpl_r_t *smpl_r = smpl_r_array + i;
+                double r = 0.0;
+                if (smpl_r->n) {
+                    double sum_crossprod = smpl_r->xy-(smpl_r->x*smpl_r->y)/smpl_r->n;//per 17.3 machine formula
+                    double x2_xx = smpl_r->x2-(smpl_r->x*smpl_r->x)/smpl_r->n;
+                    double y2_yy = smpl_r->y2-(smpl_r->y*smpl_r->y)/smpl_r->n;
+                    r = (sum_crossprod)/sqrt(x2_xx*y2_yy);
+                }
                 printf("GC%cS\t2\t%s\t%.3f",  x==0 ? 's' : 'i', args->files->samples[i], m+mm ? mm*100.0/(m+mm) : 0);
                 printf("\t%"PRId64"\t%"PRId64"\t%"PRId64"", stats[i].m[T2S(GT_HOM_RR)],stats[i].m[T2S(GT_HET_RA)],stats[i].m[T2S(GT_HOM_AA)]);
-                printf("\t%"PRId64"\t%"PRId64"\t%"PRId64"\n", stats[i].mm[T2S(GT_HOM_RR)],stats[i].mm[T2S(GT_HET_RA)],stats[i].mm[T2S(GT_HOM_AA)]);
+                printf("\t%"PRId64"\t%"PRId64"\t%"PRId64"", stats[i].mm[T2S(GT_HOM_RR)],stats[i].mm[T2S(GT_HET_RA)],stats[i].mm[T2S(GT_HOM_AA)]);
+                if (smpl_r->n && !isnan(r)) printf("\t%f\n", r*r);
+                else printf("\t"NA_STRING"\n");
             }
         }
     }
@@ -1284,19 +1391,22 @@ static void print_stats(args_t *args)
         }
 
 
-        if ( args->exons )
+        printf("# PSI, Per-Sample Indels\n# PSI\t[2]id\t[3]sample\t[4]in-frame\t[5]out-frame\t[6]not applicable\t[7]out/(in+out) ratio\t[8]nHets\t[9]nAA\n");
+        for (id=0; id<args->nstats; id++)
         {
-            printf("# PSI, Per-Sample Indels\n# PSI\t[2]id\t[3]sample\t[4]in-frame\t[5]out-frame\t[6]not applicable\t[7]out/(in+out) ratio\n");
-            for (id=0; id<args->nstats; id++)
+            stats_t *stats = &args->stats[id];
+            for (i=0; i<args->files->n_smpl; i++)
             {
-                stats_t *stats = &args->stats[id];
-                for (i=0; i<args->files->n_smpl; i++)
+                int na = 0, in = 0, out = 0;
+                if ( args->exons )
                 {
-                    int na  = stats->smpl_frm_shifts[i*3 + 0];
-                    int in  = stats->smpl_frm_shifts[i*3 + 1];
-                    int out = stats->smpl_frm_shifts[i*3 + 2];
-                    printf("PSI\t%d\t%s\t%d\t%d\t%d\t%.2f\n", id,args->files->samples[i], in,out,na,in+out?1.0*out/(in+out):0);
+                    na  = stats->smpl_frm_shifts[i*3 + 0];
+                    in  = stats->smpl_frm_shifts[i*3 + 1];
+                    out = stats->smpl_frm_shifts[i*3 + 2];
                 }
+                int nhom = stats->smpl_indel_homs[i];
+                int nhet = stats->smpl_indel_hets[i];
+                printf("PSI\t%d\t%s\t%d\t%d\t%d\t%.2f\t%d\t%d\n", id,args->files->samples[i], in,out,na,in+out?1.0*out/(in+out):0,nhet,nhom);
             }
         }
 
@@ -1355,10 +1465,12 @@ static void usage(void)
     fprintf(stderr, "    -1, --1st-allele-only              include only 1st allele at multiallelic sites\n");
     fprintf(stderr, "    -c, --collapse <string>            treat as identical records with <snps|indels|both|all|some|none>, see man page for details [none]\n");
     fprintf(stderr, "    -d, --depth <int,int,int>          depth distribution: min,max,bin size [0,500,1]\n");
-    fprintf(stderr, "    -e, --exons <file.gz>              tab-delimited file with exons for indel frameshifts (chr,from,to; 1-based, inclusive, bgzip compressed)\n");
+    fprintf(stderr, "    -e, --exclude <expr>               exclude sites for which the expression is true (see man page for details)\n");
+    fprintf(stderr, "    -E, --exons <file.gz>              tab-delimited file with exons for indel frameshifts (chr,from,to; 1-based, inclusive, bgzip compressed)\n");
     fprintf(stderr, "    -f, --apply-filters <list>         require at least one of the listed FILTER strings (e.g. \"PASS,.\")\n");
     fprintf(stderr, "    -F, --fasta-ref <file>             faidx indexed reference sequence file to determine INDEL context\n");
-    fprintf(stderr, "    -i, --split-by-ID                  collect stats for sites with ID separately (known vs novel)\n");
+    fprintf(stderr, "    -i, --include <expr>               select sites for which the expression is true (see man page for details)\n");
+    fprintf(stderr, "    -I, --split-by-ID                  collect stats for sites with ID separately (known vs novel)\n");
     fprintf(stderr, "    -r, --regions <region>             restrict to comma-separated list of regions\n");
     fprintf(stderr, "    -R, --regions-file <file>          restrict to regions listed in a file\n");
     fprintf(stderr, "    -s, --samples <list>               list of samples for sample stats, \"-\" to include all samples\n");
@@ -1383,6 +1495,8 @@ int main_vcfstats(int argc, char *argv[])
     static struct option loptions[] =
     {
         {"1st-allele-only",0,0,'1'},
+        {"include",1,0,'i'},
+        {"exclude",1,0,'e'},
         {"help",0,0,'h'},
         {"collapse",1,0,'c'},
         {"regions",1,0,'r'},
@@ -1390,17 +1504,17 @@ int main_vcfstats(int argc, char *argv[])
         {"verbose",0,0,'v'},
         {"depth",1,0,'d'},
         {"apply-filters",1,0,'f'},
-        {"exons",1,0,'e'},
+        {"exons",1,0,'E'},
         {"samples",1,0,'s'},
         {"samples-file",1,0,'S'},
-        {"split-by-ID",0,0,'i'},
+        {"split-by-ID",0,0,'I'},
         {"targets",1,0,'t'},
         {"targets-file",1,0,'T'},
         {"fasta-ref",1,0,'F'},
         {"user-tstv",1,0,'u'},
         {0,0,0,0}
     };
-    while ((c = getopt_long(argc, argv, "hc:r:R:e:s:S:d:it:T:F:f:1u:v",loptions,NULL)) >= 0) {
+    while ((c = getopt_long(argc, argv, "hc:r:R:e:s:S:d:i:t:T:F:f:1u:vIE:",loptions,NULL)) >= 0) {
         switch (c) {
             case 'u': add_user_stats(args,optarg); break;
             case '1': args->first_allele_only = 1; break;
@@ -1427,10 +1541,12 @@ int main_vcfstats(int argc, char *argv[])
             case 'f': args->files->apply_filters = optarg; break;
             case 'r': args->regions_list = optarg; break;
             case 'R': args->regions_list = optarg; regions_is_file = 1; break;
-            case 'e': args->exons_fname = optarg; break;
+            case 'E': args->exons_fname = optarg; break;
             case 's': args->samples_list = optarg; break;
             case 'S': args->samples_list = optarg; args->samples_is_file = 1; break;
-            case 'i': args->split_by_id = 1; break;
+            case 'I': args->split_by_id = 1; break;
+            case 'e': args->filter_str = optarg; args->filter_logic |= FLT_EXCLUDE; break;
+            case 'i': args->filter_str = optarg; args->filter_logic |= FLT_INCLUDE; break;
             case 'h':
             case '?': usage();
             default: error("Unknown argument: %s\n", optarg);
diff --git a/vcfview.c b/vcfview.c
index dd0e99b..ed41595 100644
--- a/vcfview.c
+++ b/vcfview.c
@@ -63,7 +63,7 @@ typedef struct _args_t
     bcf_srs_t *files;
     bcf_hdr_t *hdr, *hnull, *hsub; // original header, sites-only header, subset header
     char **argv, *format, *sample_names, *subset_fname, *targets_list, *regions_list;
-    int argc, clevel, output_type, print_header, update_info, header_only, n_samples, *imap, calc_ac;
+    int argc, clevel, n_threads, output_type, print_header, update_info, header_only, n_samples, *imap, calc_ac;
     int trim_alts, sites_only, known, novel, min_alleles, max_alleles, private_vars, uncalled, phased;
     int min_ac, min_ac_type, max_ac, max_ac_type, min_af_type, max_af_type, gt_type;
     int *ac, mac;
@@ -185,6 +185,7 @@ static void init_data(args_t *args)
                 else if (strcmp(type_list[i], "other") == 0) args->include |= VCF_OTHER;
                 else {
                     fprintf(stderr, "[E::%s] unknown type\n", type_list[i]);
+                    fprintf(stderr, "Accepted types are snps, indels, mnps, other\n");
                     exit(1);
                 }
             }
@@ -198,6 +199,7 @@ static void init_data(args_t *args)
                 else if (strcmp(type_list[i], "other") == 0) args->exclude |= VCF_OTHER;
                 else {
                     fprintf(stderr, "[E::%s] unknown type\n", type_list[i]);
+                    fprintf(stderr, "Accepted types are snps, indels, mnps, other\n");
                     exit(1);
                 }
             }
@@ -216,10 +218,13 @@ static void init_data(args_t *args)
     else if (args->output_type & FT_GZ) strcat(modew,"z");      // compressed VCF
     args->out = hts_open(args->fn_out ? args->fn_out : "-", modew);
     if ( !args->out ) error("%s: %s\n", args->fn_out,strerror(errno));
+    if ( args->n_threads ) hts_set_threads(args->out, args->n_threads);
 
     // headers: hdr=full header, hsub=subset header, hnull=sites only header
-    if (args->sites_only)
+    if (args->sites_only){
         args->hnull = bcf_hdr_subset(args->hdr, 0, 0, 0);
+        bcf_hdr_remove(args->hnull, BCF_HL_FMT, NULL);
+    }
     if (args->n_samples > 0)
     {
         args->hsub = bcf_hdr_subset(args->hdr, args->n_samples, args->samples, args->imap);
@@ -466,7 +471,7 @@ void set_allele_type (int *atype, char *atype_string)
         *atype = ALLELE_NONMAJOR;
     }
     else {
-        error("Error: allele type (%s) not recognised. Must be one of nref|alt1|minor|major|nonmajor: %s\n", atype_string);
+        error("Error: allele type not recognised. Expected one of nref|alt1|minor|major|nonmajor, got \"%s\".\n", atype_string);
     }
 }
 
@@ -486,6 +491,7 @@ static void usage(args_t *args)
     fprintf(stderr, "    -R, --regions-file <file>           restrict to regions listed in a file\n");
     fprintf(stderr, "    -t, --targets [^]<region>           similar to -r but streams rather than index-jumps. Exclude regions with \"^\" prefix\n");
     fprintf(stderr, "    -T, --targets-file [^]<file>        similar to -R but streams rather than index-jumps. Exclude regions with \"^\" prefix\n");
+    fprintf(stderr, "        --threads <int>                 number of extra output compression threads [0]\n");
     fprintf(stderr, "\n");
     fprintf(stderr, "Subset options:\n");
     fprintf(stderr, "    -a, --trim-alt-alleles        trim alternate alleles not seen in the subset\n");
@@ -522,46 +528,48 @@ int main_vcfview(int argc, char *argv[])
     args->print_header = 1;
     args->update_info = 1;
     args->output_type = FT_VCF;
+    args->n_threads = 0;
     int targets_is_file = 0, regions_is_file = 0;
 
     static struct option loptions[] =
     {
-        {"genotype",1,0,'g'},
-        {"compression-level",1,0,'l'},
-        {"header-only",0,0,'h'},
-        {"no-header",0,0,'H'},
-        {"exclude",1,0,'e'},
-        {"include",1,0,'i'},
-        {"trim-alt-alleles",0,0,'a'},
-        {"no-update",0,0,'I'},
-        {"drop-genotypes",0,0,'G'},
-        {"private",0,0,'x'},
-        {"exclude-private",0,0,'X'},
-        {"uncalled",0,0,'u'},
-        {"exclude-uncalled",0,0,'U'},
-        {"apply-filters",1,0,'f'},
-        {"known",0,0,'k'},
-        {"novel",0,0,'n'},
-        {"min-alleles",1,0,'m'},
-        {"max-alleles",1,0,'M'},
-        {"samples",1,0,'s'},
-        {"samples-file",1,0,'S'},
-        {"force-samples",0,0,1},
-        {"output-type",1,0,'O'},
-        {"output-file",1,0,'o'},
-        {"types",1,0,'v'},
-        {"exclude-types",1,0,'V'},
-        {"targets",1,0,'t'},
-        {"targets-file",1,0,'T'},
-        {"regions",1,0,'r'},
-        {"regions-file",1,0,'R'},
-        {"min-ac",1,0,'c'},
-        {"max-ac",1,0,'C'},
-        {"min-af",1,0,'q'},
-        {"max-af",1,0,'Q'},
-        {"phased",0,0,'p'},
-        {"exclude-phased",0,0,'P'},
-        {0,0,0,0}
+        {"genotype",required_argument,NULL,'g'},
+        {"compression-level",required_argument,NULL,'l'},
+        {"threads",required_argument,NULL,9},
+        {"header-only",no_argument,NULL,'h'},
+        {"no-header",no_argument,NULL,'H'},
+        {"exclude",required_argument,NULL,'e'},
+        {"include",required_argument,NULL,'i'},
+        {"trim-alt-alleles",no_argument,NULL,'a'},
+        {"no-update",no_argument,NULL,'I'},
+        {"drop-genotypes",no_argument,NULL,'G'},
+        {"private",no_argument,NULL,'x'},
+        {"exclude-private",no_argument,NULL,'X'},
+        {"uncalled",no_argument,NULL,'u'},
+        {"exclude-uncalled",no_argument,NULL,'U'},
+        {"apply-filters",required_argument,NULL,'f'},
+        {"known",no_argument,NULL,'k'},
+        {"novel",no_argument,NULL,'n'},
+        {"min-alleles",required_argument,NULL,'m'},
+        {"max-alleles",required_argument,NULL,'M'},
+        {"samples",required_argument,NULL,'s'},
+        {"samples-file",required_argument,NULL,'S'},
+        {"force-samples",no_argument,NULL,1},
+        {"output-type",required_argument,NULL,'O'},
+        {"output-file",required_argument,NULL,'o'},
+        {"types",required_argument,NULL,'v'},
+        {"exclude-types",required_argument,NULL,'V'},
+        {"targets",required_argument,NULL,'t'},
+        {"targets-file",required_argument,NULL,'T'},
+        {"regions",required_argument,NULL,'r'},
+        {"regions-file",required_argument,NULL,'R'},
+        {"min-ac",required_argument,NULL,'c'},
+        {"max-ac",required_argument,NULL,'C'},
+        {"min-af",required_argument,NULL,'q'},
+        {"max-af",required_argument,NULL,'Q'},
+        {"phased",no_argument,NULL,'p'},
+        {"exclude-phased",no_argument,NULL,'P'},
+        {NULL,0,NULL,0}
     };
     char *tmp;
     while ((c = getopt_long(argc, argv, "l:t:T:r:R:o:O:s:S:Gf:knv:V:m:M:auUhHc:C:Ii:e:xXpPq:Q:g:",loptions,NULL)) >= 0)
@@ -666,9 +674,10 @@ int main_vcfview(int argc, char *argv[])
                 else if ( !strcasecmp(optarg,"^hom") ) args->gt_type = GT_NO_HOM;
                 else if ( !strcasecmp(optarg,"^het") ) args->gt_type = GT_NO_HET;
                 else if ( !strcasecmp(optarg,"^miss") ) args->gt_type = GT_NO_MISSING;
-                else error("The argument to -g not recognised. Expected one of hom/het/^hom/^het, got \"%s\".\n", optarg);
+                else error("The argument to -g not recognised. Expected one of hom/het/miss/^hom/^het/^miss, got \"%s\".\n", optarg);
                 break;
             }
+            case  9 : args->n_threads = strtol(optarg, 0, 0); break;
             case '?': usage(args);
             default: error("Unknown argument: %s\n", optarg);
         }
diff --git a/vcmp.c b/vcmp.c
index a117cd3..8d04b89 100644
--- a/vcmp.c
+++ b/vcmp.c
@@ -26,6 +26,7 @@ THE SOFTWARE.  */
 #include <string.h>
 #include <stdlib.h>
 #include <htslib/hts.h>
+#include <ctype.h>
 #include "vcmp.h"
 
 struct _vcmp_t
@@ -53,17 +54,18 @@ int vcmp_set_ref(vcmp_t *vcmp, char *ref1, char *ref2)
     vcmp->ndref = 0;
 
     char *a = ref1, *b = ref2;
-    while ( *a && *b && *a==*b ) { a++; b++; }
+    while ( *a && *b && toupper(*a)==toupper(*b) ) { a++; b++; }
     if ( !*a && !*b ) return 0;
     if ( *a && *b ) return -1;  // refs not compatible
 
+    int i;
     if ( *a )   // ref1 is longer
     {
         vcmp->nmatch = b-ref2;
         while ( *a ) a++;
         vcmp->ndref = (a-ref1) - vcmp->nmatch;
         hts_expand(char,vcmp->ndref+1,vcmp->mdref,vcmp->dref);
-        memcpy(vcmp->dref,ref1+vcmp->nmatch,vcmp->ndref);
+        for (i=0; i<vcmp->ndref; i++) vcmp->dref[i] = toupper(ref1[vcmp->nmatch+i]);
         vcmp->dref[vcmp->ndref] = 0;
         return 0;
     }
@@ -73,7 +75,7 @@ int vcmp_set_ref(vcmp_t *vcmp, char *ref1, char *ref2)
     while ( *b ) b++;
     vcmp->ndref = (b-ref2) - vcmp->nmatch;
     hts_expand(char,vcmp->ndref+1,vcmp->mdref,vcmp->dref);
-    memcpy(vcmp->dref,ref2+vcmp->nmatch,vcmp->ndref);
+    for (i=0; i<vcmp->ndref; i++) vcmp->dref[i] = toupper(ref2[vcmp->nmatch+i]);
     vcmp->dref[vcmp->ndref] = 0;
     vcmp->ndref *= -1;
     return 0;
@@ -85,7 +87,7 @@ int vcmp_find_allele(vcmp_t *vcmp, char **als1, int nals1, char *al2)
     for (i=0; i<nals1; i++)
     {
         char *a = als1[i], *b = al2;
-        while ( *a && *b && *a==*b ) { a++; b++; }
+        while ( *a && *b && toupper(*a)==toupper(*b) ) { a++; b++; }
         if ( *a && *b ) continue;   // mismatch
         if ( !vcmp->ndref )
         {
@@ -98,14 +100,14 @@ int vcmp_find_allele(vcmp_t *vcmp, char **als1, int nals1, char *al2)
         {
             if ( vcmp->ndref<0 ) continue;
             for (j=0; j<vcmp->ndref; j++)
-                if ( !a[j] || a[j]!=vcmp->dref[j] ) break;
+                if ( !a[j] || toupper(a[j])!=vcmp->dref[j] ) break;
             if ( j!=vcmp->ndref || a[j] ) continue;
             break;  // found
         }
 
         if ( vcmp->ndref>0 ) continue;
         for (j=0; j<-vcmp->ndref; j++)
-            if ( !b[j] || b[j]!=vcmp->dref[j] ) break;
+            if ( !b[j] || toupper(b[j])!=vcmp->dref[j] ) break;
         if ( j!=-vcmp->ndref || b[j] ) continue;
         break;  // found
     }
diff --git a/version.c b/version.c
index 4a2ea7d..00eeb5a 100644
--- a/version.c
+++ b/version.c
@@ -44,4 +44,12 @@ void error(const char *format, ...)
     exit(-1);
 }
 
+const char *hts_bcf_wmode(int file_type)
+{
+    if ( file_type == FT_BCF ) return "wbu";    // uncompressed BCF
+    if ( file_type & FT_BCF ) return "wb";      // compressed BCF
+    if ( file_type & FT_GZ ) return "wz";       // compressed VCF
+    return "w";                                 // uncompressed VCF
+}
+
 

-- 
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