[med-svn] [plink1.9] 01/01: Refresh d/*
Dylan Aïssi
bob.dybian-guest at moszumanska.debian.org
Sat Jan 24 10:10:11 UTC 2015
This is an automated email from the git hooks/post-receive script.
bob.dybian-guest pushed a commit to branch master
in repository plink1.9.
commit 93e9bf7452f8517a7d30c6465d5da310b3a434b7
Author: Dylan Aïssi <bob.dybian at gmail.com>
Date: Fri Jan 23 06:34:14 2015 +0100
Refresh d/*
---
debian/control | 5 +-
debian/copyright | 30 +
debian/manpages | 2 +-
debian/patches/01_Fix_use_internal_lib.patch | 10 +-
debian/patches/02_Activate_Hardening.patch | 6 +-
debian/patches/03_Rename_binary_to_plink1.9.patch | 6 +-
debian/patches/04_Activate_Stable_Build.patch | 2 +-
debian/plink1.9.1 | 2242 ---------------------
debian/rules | 4 +
debian/tests/output_tests/{README.out => README} | 4 +-
debian/tests/run-sample-analysis | 6 +-
11 files changed, 55 insertions(+), 2262 deletions(-)
diff --git a/debian/control b/debian/control
index aa5a322..68ee2c6 100644
--- a/debian/control
+++ b/debian/control
@@ -4,6 +4,7 @@ Priority: optional
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Dylan Aïssi <bob.dybian at gmail.com>
Build-Depends: debhelper (>= 9.0.0),
+ help2man,
libatlas-base-dev,
liblapack-dev,
zlib1g-dev
@@ -26,8 +27,8 @@ Description: whole-genome association analysis toolset
disease phenotypes. The joint investigation of copy number variations is
supported. A variety of statistical tests have been implemented.
.
- plink1.9 is a comprehensive update of plink with new algorithms and new methods,
- faster and less memory consumer than the first plink.
+ plink1.9 is a comprehensive update of plink with new algorithms and new
+ methods, faster and less memory consumer than the first plink.
.
Please note: The executable was renamed to plink1.9
because of a name clash. Please read more about this
diff --git a/debian/copyright b/debian/copyright
index e963feb..2c15498 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -12,6 +12,18 @@ Files: pigz.c
Copyright: 2007-2013 Mark Adler, Christopher Chang
License: Zlib
+Files: Rconnection.cc
+Copyright: 2004-8 Simon Urbanek
+License: LGPL-2.1
+
+Files: Rsrv.h
+Copyright: 2002-13 Simon Urbanek
+License: LGPL-2.1
+
+Files: sisocks.h
+Copyright: 2000,1 Simon Urbanek
+License: LGPL-2.1
+
Files: SFMT.*
Copyright: 2006-2012 Mutsuo Saito, Makoto Matsumoto, Hiroshima University and The University of Tokyo
License: BSD-3-clause
@@ -75,6 +87,24 @@ License: Zlib
misrepresented as being the original software.
3. This notice may not be removed or altered from any source distribution.
+License: LGPL-2.1
+ This program is free software; you can redistribute it and/or modify
+ it under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation; version 2.1 of the License
+ .
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU Leser General Public License for more details.
+ .
+ You should have received a copy of the GNU Lesser General Public License
+ along with this program; if not, write to the Free Software
+ Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301, USA.
+ .
+ Although this code is licensed under LGPL v2.1, we strongly encourage
+ everyone modifying this software to contribute back any improvements and
+ bugfixes to the project for the benefit all other users. Thank you.
+
License: BSD-3-clause
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
diff --git a/debian/manpages b/debian/manpages
index 0f65186..f7e585b 100644
--- a/debian/manpages
+++ b/debian/manpages
@@ -1 +1 @@
-debian/*.1
+*.1
diff --git a/debian/patches/01_Fix_use_internal_lib.patch b/debian/patches/01_Fix_use_internal_lib.patch
index 021b476..56070a5 100644
--- a/debian/patches/01_Fix_use_internal_lib.patch
+++ b/debian/patches/01_Fix_use_internal_lib.patch
@@ -1,6 +1,6 @@
Author: Dylan Aïssi <bob.dybian at gmail.com>
Description: Fix the use of Debian internal libraries.
-Last-Update: 2014-11-25
+Last-Update: 2015-01-23
Forwarded: No
--- a/Makefile
@@ -10,16 +10,16 @@ Forwarded: No
CFLAGS=-Wall -O2
-BLASFLAGS=-L/usr/lib64/atlas -llapack -lcblas -latlas
--LINKFLAGS=-lm -lpthread
+-LINKFLAGS=-lm -lpthread -ldl
-ZLIB=zlib-1.2.8/libz.so.1.2.8
+BLASFLAGS=-llapack -lcblas -latlas
-+LINKFLAGS=-lm -lpthread -lz
++LINKFLAGS=-lm -lpthread -ldl -lz
+#ZLIB=zlib-1.2.8/libz.so.1.2.8
ifeq ($(SYS), MAC)
GCC_GTEQ_43 := $(shell expr `g++ -dumpversion | sed -e 's/\.\([0-9][0-9]\)/\1/g' -e 's/\.\([0-9]\)/0\1/g' -e 's/^[0-9]\{3,4\}$$/&00/'` \>= 40300)
-@@ -55,8 +55,9 @@
- # either renaming that binary to "plink1" or this one to "plink2".
+@@ -57,8 +57,9 @@
+ # lead to minor problems when PLINK 2.0 is released.)
plink: $(SRC)
- g++ $(CFLAGS) $(SRC) -o plink $(BLASFLAGS) $(LINKFLAGS) -L. $(ZLIB)
diff --git a/debian/patches/02_Activate_Hardening.patch b/debian/patches/02_Activate_Hardening.patch
index a6c29ce..d7627ed 100644
--- a/debian/patches/02_Activate_Hardening.patch
+++ b/debian/patches/02_Activate_Hardening.patch
@@ -1,12 +1,12 @@
Author: Dylan Aïssi <bob.dybian at gmail.com>
Description: Activate Hardening FLAGs.
-Last-Update: 2014-11-25
+Last-Update: 2015-01-23
Forwarded: No
--- a/Makefile
+++ b/Makefile
-@@ -55,9 +55,9 @@
- # either renaming that binary to "plink1" or this one to "plink2".
+@@ -57,9 +57,9 @@
+ # lead to minor problems when PLINK 2.0 is released.)
plink: $(SRC)
- g++ $(CFLAGS) $(SRC) -o plink $(BLASFLAGS) $(LINKFLAGS)
diff --git a/debian/patches/03_Rename_binary_to_plink1.9.patch b/debian/patches/03_Rename_binary_to_plink1.9.patch
index a196013..d5f184e 100644
--- a/debian/patches/03_Rename_binary_to_plink1.9.patch
+++ b/debian/patches/03_Rename_binary_to_plink1.9.patch
@@ -1,12 +1,12 @@
Author: Dylan Aïssi <bob.dybian at gmail.com>
Description: Rename binary from plink to plink1.9 to avoid name conflict with the first plink and the plink from ssh clone putty.
-Last-Update: 2014-12-22
+Last-Update: 2015-01-23
Forwarded: https://github.com/chrchang/plink-ng/issues/12
--- a/Makefile
+++ b/Makefile
-@@ -55,9 +55,9 @@
- # either renaming that binary to "plink1" or this one to "plink2".
+@@ -57,9 +57,9 @@
+ # lead to minor problems when PLINK 2.0 is released.)
plink: $(SRC)
- g++ $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) $(SRC) -o plink $(BLASFLAGS) $(LINKFLAGS)
diff --git a/debian/patches/04_Activate_Stable_Build.patch b/debian/patches/04_Activate_Stable_Build.patch
index 4f2aed9..3968e78 100644
--- a/debian/patches/04_Activate_Stable_Build.patch
+++ b/debian/patches/04_Activate_Stable_Build.patch
@@ -1,6 +1,6 @@
Author: Dylan Aïssi <bob.dybian at gmail.com>
Description: Activate stable build.
-Last-Update: 2014-12-22
+Last-Update: 2015-01-23
Forwarded: No
--- a/plink_common.h
diff --git a/debian/plink1.9.1 b/debian/plink1.9.1
deleted file mode 100644
index da99d76..0000000
--- a/debian/plink1.9.1
+++ /dev/null
@@ -1,2242 +0,0 @@
-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.40.10.
-.TH PLINK "1" "December 2014" "PLINK v1.90b2t 64-bit (20 Dec 2014)" "User Commands"
-.SH NAME
-PLINK2 \- manual page for PLINK v1.90b2t 64-bit (20 Dec 2014)
-.SH DESCRIPTION
-PLINK v1.90b2t 64\-bit (20 Dec 2014) https://www.cog\-genomics.org/plink2
-(C) 2005\-2014 Shaun Purcell, Christopher Chang GNU General Public License v3
-.PP
-In the command line flag definitions that follow,
-.IP
-* [square brackets] denote a required parameter, where the text between the
-.IP
-brackets describes its nature.
-.IP
-* <angle brackets> denote an optional modifier (or if '|' is present, a set
-.TP
-of mutually exclusive optional modifiers).
-Use the EXACT text in the
-.IP
-definition, e.g. '\-\-dummy acgt'.
-.IP
-* There's one exception to the angle brackets/exact text rule: when an angle
-.IP
-bracket term ends with '=[value]', '[value]' designates a variable
-parameter.
-.IP
-* {curly braces} denote an optional parameter, where the text between the
-.IP
-braces describes its nature.
-.IP
-* An ellipsis (...) indicates that you may enter multiple parameters of the
-.IP
-specified type.
-.IP
-plink [input flag(s)...] {command flag(s)...} {other flag(s)...}
-plink \fB\-\-help\fR {flag name(s)...}
-.PP
-Most PLINK runs require exactly one main input fileset. The following flags
-are available for defining its form and location:
-.HP
-\fB\-\-bfile\fR {prefix} : Specify .bed + .bim + .fam prefix (default 'plink').
-.HP
-\fB\-\-bed\fR [filename] : Specify full name of .bed file.
-.HP
-\fB\-\-bim\fR [filename] : Specify full name of .bim file.
-.HP
-\fB\-\-fam\fR [filename] : Specify full name of .fam file.
-.TP
-\fB\-\-keep\-autoconv\fR
-: With \fB\-\-file\fR/\-\-tfile/\-\-lfile/\-\-vcf/\-\-bcf/\-\-data/\-\-23file,
-don't delete autogenerated binary fileset at end of run.
-.TP
-\fB\-\-file\fR {prefix}
-: Specify .ped + .map filename prefix (default 'plink').
-.HP
-\fB\-\-ped\fR [filename] : Specify full name of .ped file.
-.HP
-\fB\-\-map\fR [filename] : Specify full name of .map file.
-.TP
-\fB\-\-no\-fid\fR
-: .fam/.ped file does not contain column 1 (family ID).
-.TP
-\fB\-\-no\-parents\fR
-: .fam/.ped file does not contain columns 3\-4 (parents).
-.TP
-\fB\-\-no\-sex\fR
-: .fam/.ped file does not contain column 5 (sex).
-.TP
-\fB\-\-no\-pheno\fR
-: .fam/.ped file does not contain column 6 (phenotype).
-.HP
-\fB\-\-tfile\fR {prefix} : Specify .tped + .tfam filename prefix (default 'plink').
-.TP
-\fB\-\-tped\fR [fname]
-: Specify full name of .tped file.
-.TP
-\fB\-\-tfam\fR [fname]
-: Specify full name of .tfam file.
-.HP
-\fB\-\-lfile\fR {prefix} : Specify .lgen + .map + .fam (long\-format fileset) prefix.
-.HP
-\fB\-\-reference\fR [fn] : Specify default allele file accompanying \fB\-\-lfile\fR input.
-.TP
-\fB\-\-allele\-count\fR
-: When used with \fB\-\-lfile\fR + \fB\-\-reference\fR, specifies that the
-\&.lgen file contains reference allele counts.
-.HP
-\fB\-\-vcf\fR [filename] : Specify full name of .vcf or .vcf.gz file.
-.HP
-\fB\-\-bcf\fR [filename] : Specify full name of BCF2 file.
-.TP
-\fB\-\-data\fR {prefix}
-: Specify Oxford .gen + .sample prefix (default 'plink').
-.HP
-\fB\-\-gen\fR [filename] : Specify full name of .gen or .gen.gz file.
-.HP
-\fB\-\-bgen\fR [f] <snpid\-chr> : Specify full name of .bgen file.
-.HP
-\fB\-\-sample\fR [fname] : Specify full name of .sample file.
-.HP
-\fB\-\-23file\fR [fname] {FID} {IID} {sex} {pheno} {pat. ID} {mat. ID} :
-.IP
-Specify 23andMe input file.
-.TP
-\fB\-\-grm\-gz\fR {prfx}
-: Specify .grm.gz + .grm.id (GCTA rel. matrix) prefix.
-.TP
-\fB\-\-grm\-bin\fR {prfx} : Specify .grm.bin + .grm.N.bin + .grm.id (GCTA triangular
-binary relationship matrix) filename prefix.
-.HP
-\fB\-\-dummy\fR [sample ct] [SNP ct] {missing geno freq} {missing pheno freq}
-.IP
-<acgt | 1234 | 12> <scalar\-pheno>
-.IP
-This generates a fake input dataset with the specified number of samples
-and SNPs. By default, the missing genotype and phenotype frequencies are
-zero, and genotypes are As and Bs (change the latter with
-\&'acgt'/'1234'/'12'). The 'scalar\-pheno' modifier causes a normally
-distributed scalar phenotype to be generated instead of a binary one.
-.HP
-\fB\-\-simulate\fR [simulation parameter file] <tags | haps> <acgt | 1234 | 12>
-.HP
-\fB\-\-simulate\-qt\fR [simulation parameter file] <tags | haps> <acgt | 1234 | 12>
-.HP
-\fB\-\-simulate\fR generates a fake input dataset with disease\-associated SNPs,
-.IP
-while \fB\-\-simulate\-qt\fR generates a dataset with quantitative trait loci.
-.PP
-Output files have names of the form 'plink.{extension}' by default. You can
-change the 'plink' prefix with
-.TP
-\fB\-\-out\fR [prefix]
-: Specify prefix for output files.
-.PP
-Most runs also require at least one of the following commands:
-.HP
-\fB\-\-make\-bed\fR
-.TP
-Create a new binary fileset.
-Unlike the automatic text\-to\-binary
-.IP
-converters (which only heed chromosome filters), this supports all of
-PLINK's filtering flags.
-.HP
-\fB\-\-make\-just\-bim\fR
-.HP
-\fB\-\-make\-just\-fam\fR
-.TP
-Variants of \fB\-\-make\-bed\fR which only write a new .bim or .fam file.
-Can be
-.IP
-used with only .bim/.fam input.
-USE THESE CAUTIOUSLY. It is very easy to desynchronize your binary
-genotype data and your .bim/.fam indexes if you use these commands
-improperly. If you have any doubt, stick with \fB\-\-make\-bed\fR.
-.HP
-\fB\-\-recode\fR <01 | 12> <23 | A{\-transpose} | AD | beagle{\-nomap} | bimbam{\-1chr}
-.IP
-| compound\-genotypes | fastphase{\-1chr} | HV{\-1chr} | lgen{\-ref} |
-list | oxford | rlist | structure | transpose | vcf | vcf\-fid |
-vcf\-iid> <tab | tabx | spacex> <include\-alt>
-.TP
-Create a new text fileset with all filters applied.
-By default, the
-.IP
-fileset consists of a .ped and a .map file, readable with \fB\-\-file\fR.
-* The '12' modifier causes A1 (usually minor) alleles to be coded as '1'
-.IP
-and A2 alleles to be coded as '2', while '01' maps A1 \-> 0 and A2 \-> 1.
-.TP
-* The '23' modifier causes a 23andMe\-formatted file to be generated.
-This
-.IP
-can only be used on a single sample's data (\fB\-\-keep\fR may be handy).
-.IP
-* The 'AD' modifier causes an sample\-major additive (0/1/2) + dominant
-.IP
-(het = 1, otherwise 0) component file, suitable for loading from R, to be
-generated. If you don't want the dominant component, use 'A' instead.
-If you need uncounted alleles to be named in the header line, add the
-\&'include\-alt' modifier.
-.IP
-* The 'A\-transpose' modifier causes a variant\-major additive component file
-.IP
-to be generated.
-.IP
-* The 'beagle' modifier causes unphased per\-autosome .dat and .map files,
-.IP
-readable by early BEAGLE versions, to be generated, while 'beagle\-nomap'
-generates a single .beagle.dat file.
-.IP
-* The 'bimbam' modifier causes a BIMBAM\-formatted fileset to be generated.
-.IP
-If your input data only contains one chromosome, you can use
-\&'bimbam\-1chr' instead to write a two\-column .pos.txt file.
-.IP
-* The 'compound\-genotypes' modifier removes the space between pairs of
-.IP
-allele codes for the same variant when generating a .ped + .map fileset.
-.IP
-* The 'fastphase' modifier causes per\-chromosome fastPHASE files to be
-.TP
-generated.
-If your input data only contains one chromosome, you can use
-.IP
-\&'fastphase\-1chr' instead to exclude the chromosome number from the file
-extension.
-.IP
-* The 'HV' modifier causes a Haploview\-format .ped + .info fileset to be
-.TP
-generated per chromosome.
-\&'HV\-1chr' is analogous to 'fastphase\-1chr'.
-.IP
-* The 'lgen' modifier causes a long\-format fileset (loadable with \fB\-\-lfile\fR)
-.IP
-to be generated, while 'lgen\-ref' generates a (usually) smaller
-long\-format fileset loadable with \fB\-\-lfile\fR + \fB\-\-reference\fR.
-.IP
-* The 'list' modifier creates a genotype\-based list, while 'rlist' creates
-.IP
-a rare\-genotype fileset.
-.IP
-* 'oxford' causes an Oxford\-format .gen + .sample fileset to be generated.
-* The 'structure' modifier causes a Structure\-format file to be generated.
-* 'transpose' creates a transposed text fileset (loadable with \fB\-\-tfile\fR).
-* 'vcf', 'vcf\-fid', and 'vcf\-iid' result in production of a VCFv4.1 file.
-.IP
-\&'vcf\-fid' and 'vcf\-iid' cause family IDs or within\-family IDs
-respectively to be used for the sample IDs in the last header row, while
-\&'vcf' merges both IDs and puts an underscore between them. The A2 allele
-is saved as the reference; when it is important for reference alleles to
-be correct, you'll usually also want to include \fB\-\-a2\-allele\fR in your
-command.
-.IP
-* The 'tab' modifier makes the output mostly tab\-delimited instead of
-.TP
-mostly space\-delimited.
-\&'tabx' and 'spacex' force all tabs and all
-.IP
-spaces, respectively.
-.HP
-\fB\-\-flip\-scan\fR <verbose>
-.IP
-(alias: \fB\-\-flipscan\fR)
-LD\-based scan for case/control strand inconsistency.
-.HP
-\fB\-\-write\-covar\fR
-.IP
-If a \fB\-\-covar\fR file is loaded, \fB\-\-make\-bed\fR/\-\-make\-just\-fam and \fB\-\-recode\fR
-automatically generate an updated version (with all filters applied).
-However, if you do not wish to simultaneously generate a new genotype file,
-you can use \fB\-\-write\-covar\fR to just produce a pruned covariate file.
-.HP
-\fB\-\-write\-cluster\fR <omit\-unassigned>
-.IP
-If clusters are specified with \fB\-\-within\fR/\-\-family, this generates a new
-cluster file (with all filters applied). The 'omit\-unassigned' modifier
-causes unclustered samples to be omitted from the file; otherwise their
-cluster is 'NA'.
-.HP
-\fB\-\-write\-set\fR
-.HP
-\fB\-\-set\-table\fR
-.IP
-If sets have been defined, \fB\-\-write\-set\fR dumps 'END'\-terminated set
-membership lists to {output prefix}.set, while \fB\-\-set\-table\fR writes a
-variant\-by\-set membership table to {output prefix}.set.table.
-.HP
-\fB\-\-merge\fR [.ped filename] [.map filename]
-.HP
-\fB\-\-merge\fR [text fileset prefix]
-.HP
-\fB\-\-bmerge\fR [.bed filename] [.bim filename] [.fam filename]
-.HP
-\fB\-\-bmerge\fR [binary fileset prefix]
-.IP
-Merge the given fileset with the initially loaded fileset, writing the
-result to {output prefix}.bed + .bim + .fam. (It is no longer necessary to
-simultaneously specify \fB\-\-make\-bed\fR.)
-.HP
-\fB\-\-merge\-list\fR [filename]
-.IP
-Merge all filesets named in the text file with the reference fileset, if
-one was specified. (However, this can also be used *without* a reference;
-in that case, the newly created fileset is then treated as the reference by
-most other PLINK operations.) The text file is interpreted as follows:
-* If a line contains only one name, it is assumed to be the prefix for a
-.IP
-binary fileset.
-.IP
-* If a line contains exactly two names, they are assumed to be the full
-.IP
-filenames for a text fileset (.ped first, then .map).
-.IP
-* If a line contains exactly three names, they are assumed to be the full
-.IP
-filenames for a binary fileset (.bed, then .bim, then .fam).
-.HP
-\fB\-\-write\-snplist\fR
-.HP
-\fB\-\-list\-23\-indels\fR
-.HP
-\fB\-\-write\-snplist\fR writes a .snplist file listing the names of all variants
-.IP
-which pass the filters and inclusion thresholds you've specified, while
-\fB\-\-list\-23\-indels\fR writes the subset with 23andMe\-style indel calls (D/I
-allele codes).
-.HP
-\fB\-\-freq\fR <counts>
-.HP
-\fB\-\-freqx\fR
-.HP
-\fB\-\-freq\fR generates a basic allele frequency (or count, if the 'counts'
-.TP
-modifier is present) report.
-This can be combined with \fB\-\-within\fR/\-\-family
-.IP
-to produce a cluster\-stratified allele frequency/count report instead.
-\fB\-\-freqx\fR generates a more detailed genotype count report, designed for use
-with \fB\-\-read\-freq\fR.
-.HP
-\fB\-\-missing\fR
-.TP
-Generate sample\- and variant\-based missing data reports.
-If clusters are
-.IP
-defined, the variant\-based report is cluster\-stratified.
-.HP
-\fB\-\-test\-mishap\fR
-.IP
-Check for association between missing calls and flanking haplotypes.
-.HP
-\fB\-\-hardy\fR <midp>
-.TP
-Generate a Hardy\-Weinberg exact test p\-value report.
-(This does NOT
-.TP
-simultaneously filter on the p\-value any more; use \fB\-\-hwe\fR for that.)
-With
-.IP
-the 'midp' modifier, the test applies the mid\-p adjustment described in
-Graffelman J, Moreno V (2013) The mid p\-value in exact tests for
-Hardy\-Weinberg Equilibrium.
-.HP
-\fB\-\-mendel\fR
-.IP
-Generate a Mendel error report.
-.HP
-\fB\-\-het\fR <small\-sample>
-.HP
-\fB\-\-ibc\fR
-.TP
-Estimate inbreeding coefficients.
-\fB\-\-het\fR reports method\-of\-moments
-.IP
-estimates, while \fB\-\-ibc\fR calculates all three values described in Yang J, Lee
-SH, Goddard ME and Visscher PM (2011) GCTA: A Tool for Genome\-wide Complex
-Trait Analysis. (That paper also describes the relationship matrix
-computation we reimplement.)
-* These functions require decent MAF estimates. If there are very few
-.IP
-samples in your immediate fileset, \fB\-\-read\-freq\fR is practically mandatory
-since imputed MAFs are wildly inaccurate in that case.
-.IP
-* They also assume the marker set is in approximate linkage equilibrium.
-* By default, \fB\-\-het\fR omits the n/(n\-1) multiplier in Nei's expected
-.TP
-homozygosity formula.
-The 'small\-sample' modifier causes it to be
-.IP
-included, while forcing \fB\-\-het\fR to use MAFs imputed from founders in the
-immediate dataset.
-.HP
-\fB\-\-check\-sex\fR {female max F} {male min F}
-.TP
-\fB\-\-check\-sex\fR ycount {female max F} {male min F} {female max Y obs}
-{male min Y obs}
-.HP
-\fB\-\-check\-sex\fR y\-only {female max Y obs} {male min Y obs}
-.HP
-\fB\-\-impute\-sex\fR {female max F} {male min F}
-.TP
-\fB\-\-impute\-sex\fR ycount {female max F} {male min F} {female max Y obs}
-{male min Y obs}
-.HP
-\fB\-\-impute\-sex\fR y\-only {female max Y obs} {male min Y obs}
-.HP
-\fB\-\-check\-sex\fR normally compares sex assignments in the input dataset with
-.IP
-those imputed from X chromosome inbreeding coefficients.
-* Make sure that the X chromosome pseudo\-autosomal region has been split
-.IP
-off (with e.g. \fB\-\-split\-x\fR) before using this.
-.IP
-* You also need decent MAF estimates (so, with very few samples in your
-.IP
-immediate fileset, use \fB\-\-read\-freq\fR), and your marker set should be in
-approximate linkage equilibrium.
-.IP
-* By default, F estimates smaller than 0.2 yield female calls, and values
-.TP
-larger than 0.8 yield male calls.
-If you pass numeric parameter(s) to
-.HP
-\fB\-\-check\-sex\fR, the first two control these thresholds.
-.IP
-There are now two modes which consider Y chromosome data.
-* In 'ycount' mode, gender is still imputed from the X chromosome, but
-.IP
-female calls are downgraded to ambiguous whenever more than 0 nonmissing
-Y genotypes are present, and male calls are downgraded when fewer than 0
-are present. (Note that these are counts, not rates.) These thresholds
-are controllable with \fB\-\-check\-sex\fR ycount's optional 3rd and 4th numeric
-parameters.
-.IP
-* In 'y\-only' mode, gender is imputed from nonmissing Y genotype counts.
-.IP
-The male minimum threshold defaults to 1 instead of zero in this case.
-.HP
-\fB\-\-impute\-sex\fR changes sex assignments to the imputed values, and is
-.TP
-otherwise identical to \fB\-\-check\-sex\fR.
-It must be used with
-.HP
-\fB\-\-make\-bed\fR/\-\-recode/\-\-write\-covar.
-.HP
-\fB\-\-fst\fR <case\-control>
-.IP
-(alias: \fB\-\-Fst\fR)
-Estimate Wright's Fst for each autosomal diploid variant using the method
-introduced in Weir BS, Cockerham CC (1984) Estimating F\-statistics for the
-analysis of population structure, given a set of subpopulations defined via
-\fB\-\-within\fR. Raw and weighted global means are also reported.
-* If you're interested in the global means, it is usually best to perform
-.IP
-this calculation on a marker set in approximate linkage equilibrium.
-.IP
-* If you have only two subpopulations, you can represent them with
-.IP
-case/control status and use the 'case\-control' modifier.
-.HP
-\fB\-\-indep\fR [window size]<kb> [step size (variant ct)] [VIF threshold]
-.HP
-\fB\-\-indep\-pairwise\fR [window size]<kb> [step size (variant ct)] [r^2 threshold]
-.HP
-\fB\-\-indep\-pairphase\fR [window size]<kb> [step size (variant ct)] [r^2 threshold]
-.TP
-Generate a list of markers in approximate linkage equilibrium.
-With the
-.IP
-\&'kb' modifier, the window size is in kilobase instead of variant count
-units. (Pre\-'kb' space is optional, i.e. '\-\-indep\-pairwise 500 kb 5 0.5'
-and '\-\-indep\-pairwise 500kb 5 0.5' have the same effect.)
-Note that you need to rerun PLINK using \fB\-\-extract\fR or \fB\-\-exclude\fR on the
-\&.prune.in/.prune.out file to apply the list to another computation.
-.HP
-\fB\-\-r\fR <square | square0 | triangle | inter\-chr> <gz | bin | bin4> <spaces>
-.IP
-<in\-phase> <dprime> <with\-freqs> <yes\-really>
-.HP
-\fB\-\-r2\fR <square | square0 | triangle | inter\-chr> <gz | bin | bin4> <spaces>
-.IP
-<in\-phase> <dprime> <with\-freqs> <yes\-really>
-.TP
-LD statistic reports.
-\fB\-\-r\fR yields raw inter\-variant correlations, while
-.TP
-\fB\-\-r2\fR reports their squares.
-You can request results for all pairs in
-.IP
-matrix format (if you specify 'bin' or one of the shape modifiers), all
-pairs in table format ('inter\-chr'), or a limited window in table format
-(default).
-* The 'gz' modifier causes the output text file to be gzipped.
-* 'bin' causes the output matrix to be written in double\-precision binary
-.TP
-format, while 'bin4' specifics single\-precision binary.
-The matrix is
-.IP
-square if no shape is explicitly specified.
-.IP
-* By default, text matrices are tab\-delimited; 'spaces' switches this.
-* 'in\-phase' adds a column with in\-phase allele pairs to table\-formatted
-.TP
-reports.
-(This cannot be used with very long allele codes.)
-.IP
-* 'dprime' adds Lewontin's D\-prime statistic to table\-formatted reports,
-.IP
-and forces both r/r^2 and D\-prime to be based on the maximum likelihood
-solution to the cubic equation discussed in Gaunt T, Rodriguez S, Day I
-(2007) Cubic exact solutions for the estimation of pairwise haplotype
-frequencies.
-.IP
-* 'with\-freqs' adds MAF columns to table\-formatted reports.
-* Since the resulting file can easily be huge, you're required to add the
-.IP
-\&'yes\-really' modifier when requesting an unfiltered, non\-distributed all
-pairs computation on more than 400k variants.
-.IP
-* These computations can be subdivided with \fB\-\-parallel\fR (even when the
-.IP
-\&'square' modifier is active).
-.HP
-\fB\-\-ld\fR [variant ID] [variant ID] <hwe\-midp>
-.IP
-This displays haplotype frequencies, r^2, and D' for a single pair of
-variants. When there are multiple biologically possible solutions to the
-haplotype frequency cubic equation, all are displayed (instead of just the
-maximum likelihood solution identified by \fB\-\-r\fR/\-\-r2), along with HWE exact
-test statistics.
-.HP
-\fB\-\-blocks\fR <no\-pheno\-req> <no\-small\-max\-span>
-.IP
-Estimate haplotype blocks, via Haploview's interpretation of the block
-definition suggested by Gabriel S et al. (2002) The Structure of Haplotype
-Blocks in the Human Genome.
-* Normally, samples with missing phenotypes are not considered by this
-.IP
-computation; the 'no\-pheno\-req' modifier lifts this restriction.
-.IP
-* Normally, size\-2 blocks may not span more than 20kb, and size\-3 blocks
-.TP
-are limited to 30kb.
-The 'no\-small\-max\-span' modifier removes these
-.IP
-limits.
-.TP
-The .blocks file is valid input for PLINK 1.07's \fB\-\-hap\fR command.
-However,
-.IP
-the \fB\-\-hap\fR... family of flags has not been reimplemented in PLINK 1.9 due to
-poor phasing accuracy relative to other software; for now, we recommend
-using BEAGLE instead of PLINK for case/control haplotype association
-analysis. (You can use '\-\-recode beagle' to export data to BEAGLE 3.3.)
-We apologize for the inconvenience, and plan to develop variants of the
-\fB\-\-hap\fR... flags which handle pre\-phased data effectively.
-.HP
-\fB\-\-distance\fR <square | square0 | triangle> <gz | bin | bin4> <ibs> <1\-ibs>
-.IP
-<allele\-ct> <flat\-missing>
-.IP
-Write a lower\-triangular tab\-delimited table of (weighted) genomic
-distances in allele count units to {output prefix}.dist, and a list of the
-corresponding sample IDs to {output prefix}.dist.id. The first row of the
-\&.dist file contains a single {genome 1\-genome 2} distance, the second row
-has the {genome 1\-genome 3} and {genome 2\-genome 3} distances in that
-order, etc.
-* It is usually best to perform this calculation on a marker set in
-.IP
-approximate linkage equilibrium.
-.IP
-* If the 'square' or 'square0' modifier is present, a square matrix is
-.IP
-written instead; 'square0' fills the upper right triangle with zeroes.
-.IP
-* If the 'gz' modifier is present, a compressed .dist.gz file is written
-.IP
-instead of a plain text file.
-.IP
-* If the 'bin' modifier is present, a binary (square) matrix of
-.IP
-double\-precision floating point values, suitable for loading from R, is
-instead written to {output prefix}.dist.bin. ('bin4' specifies
-single\-precision numbers instead.) This can be combined with 'square0'
-if you still want the upper right zeroed out, or 'triangle' if you don't
-want to pad the upper right at all.
-.IP
-* If the 'ibs' modifier is present, an identity\-by\-state matrix is written
-.TP
-to {output prefix}.mibs.
-\&'1\-ibs' causes distances expressed as genomic
-.IP
-proportions (i.e. 1 \- IBS) to be written to {output prefix}.mdist.
-Combine with 'allele\-ct' if you want to generate the usual .dist file as
-well.
-.IP
-* By default, distance rescaling in the presence of missing genotype calls
-.IP
-is sensitive to allele count distributions: if variant A contributes, on
-average, twice as much to other pairwise distances as variant B, a
-missing call at variant A will result in twice as large of a missingness
-correction. To turn this off (because e.g. your missing calls are highly
-nonrandom), use the 'flat\-missing' modifier.
-.IP
-* The computation can be subdivided with \fB\-\-parallel\fR.
-.HP
-\fB\-\-distance\-matrix\fR
-.HP
-\fB\-\-ibs\-matrix\fR
-.IP
-These deprecated commands are equivalent to '\-\-distance 1\-ibs flat\-missing
-square' and '\-\-distance ibs flat\-missing square', respectively, except that
-they generate space\- instead of tab\-delimited text matrices.
-.HP
-\fB\-\-make\-rel\fR <square | square0 | triangle> <gz | bin | bin4>
-.IP
-<cov | ibc2 | ibc3>
-.IP
-Write a lower\-triangular variance\-standardized realized relationship matrix
-to {output prefix}.rel, and corresponding IDs to {output prefix}.rel.id.
-* It is usually best to perform this calculation on a marker set in
-.IP
-approximate linkage equilibrium.
-.IP
-* 'square', 'square0', 'triangle', 'gz', 'bin', and 'bin4' act as they do
-.IP
-on \fB\-\-distance\fR.
-.IP
-* The 'cov' modifier removes the variance standardization step, causing a
-.IP
-covariance matrix to be calculated instead.
-.IP
-* By default, the diagonal elements in the relationship matrix are based on
-.HP
-\fB\-\-ibc\fR's Fhat1; use the 'ibc2' or 'ibc3' modifiers to base them on Fhat2
-.IP
-or Fhat3 instead.
-.IP
-* The computation can be subdivided with \fB\-\-parallel\fR.
-.HP
-\fB\-\-make\-grm\-gz\fR <no\-gz> <cov | ibc2 | ibc3>
-.HP
-\fB\-\-make\-grm\-bin\fR <cov | ibc2 | ibc3>
-.HP
-\fB\-\-make\-grm\-gz\fR writes the relationships in GCTA's original gzipped list
-.IP
-format, which describes one pair per line, while \fB\-\-make\-grm\-bin\fR writes them
-in GCTA 1.1+'s single\-precision triangular binary format. Note that these
-formats explicitly report the number of valid observations (where neither
-sample has a missing call) for each pair, which is useful input for some
-scripts.
-These computations can be subdivided with \fB\-\-parallel\fR.
-.HP
-\fB\-\-rel\-cutoff\fR {val}
-.IP
-(alias: \fB\-\-grm\-cutoff\fR)
-Exclude one member of each pair of samples with relatedness greater than
-the given cutoff value (default 0.025). If no later operation will cause
-the list of remaining samples to be written to disk, this will save it to
-{output prefix}.rel.id.
-Note that maximizing the remaining sample size is equivalent to the NP\-hard
-maximum independent set problem, so we use a greedy algorithm instead of
-guaranteeing optimality. (Use the \fB\-\-make\-rel\fR and \fB\-\-keep\fR/\-\-remove flags if
-you want to try to do better.)
-.HP
-\fB\-\-ibs\-test\fR {permutation count}
-.HP
-\fB\-\-groupdist\fR {iters} {d}
-.IP
-Given case/control phenotype data, these commands consider three subsets of
-the distance matrix: pairs of affected samples, affected\-unaffected pairs,
-and pairs of unaffected samples. Each of these subsets has a distribution
-of pairwise genomic distances; \fB\-\-ibs\-test\fR uses permutation to estimate
-p\-values re: which types of pairs are most similar, while \fB\-\-groupdist\fR
-focuses on the differences between the centers of these distributions and
-estimates standard errors via delete\-d jackknife.
-.HP
-\fB\-\-regress\-distance\fR {iters} {d}
-.IP
-Linear regression of pairwise genomic distances on pairwise average
-phenotypes and vice versa, using delete\-d jackknife for standard errors. A
-scalar phenotype is required.
-* With less than two parameters, d is set to {number of people}^0.6 rounded
-.TP
-down.
-With no parameters, 100k iterations are run.
-.HP
-\fB\-\-regress\-rel\fR {iters} {d}
-.IP
-Linear regression of pairwise genomic relationships on pairwise average
-phenotypes, and vice versa. Defaults for iters and d are the same as for
-\fB\-\-regress\-distance\fR.
-.HP
-\fB\-\-genome\fR <gz> <rel\-check> <full> <unbounded> <nudge>
-.IP
-Generate an identity\-by\-descent report.
-* It is usually best to perform this calculation on a marker set in
-.IP
-approximate linkage equilibrium.
-.IP
-* The 'rel\-check' modifier excludes pairs of samples with different FIDs
-.IP
-from the final report.
-.IP
-* 'full' adds raw pairwise comparison data to the report.
-* The P(IBD=0/1/2) estimator employed by this command sometimes yields
-.TP
-numbers outside the range [0,1]; by default, these are clipped.
-The
-.IP
-\&'unbounded' modifier turns off this clipping.
-.IP
-* Then, when PI_HAT^2 < P(IBD=2), 'nudge' adjusts the final P(IBD=0/1/2)
-.IP
-estimates to a theoretically possible configuration.
-.IP
-* The computation can be subdivided with \fB\-\-parallel\fR.
-.HP
-\fB\-\-homozyg\fR <group | group\-verbose> <consensus\-match> <extend>
-.IP
-<subtract\-1\-from\-lengths>
-.HP
-\fB\-\-homozyg\-snp\fR [min var count]
-.HP
-\fB\-\-homozyg\-kb\fR [min length]
-.HP
-\fB\-\-homozyg\-density\fR [max inverse density (kb/var)]
-.HP
-\fB\-\-homozyg\-gap\fR [max internal gap kb length]
-.HP
-\fB\-\-homozyg\-het\fR [max hets]
-.HP
-\fB\-\-homozyg\-window\-snp\fR [scanning window size]
-.HP
-\fB\-\-homozyg\-window\-het\fR [max hets in scanning window hit]
-.HP
-\fB\-\-homozyg\-window\-missing\fR [max missing calls in scanning window hit]
-.HP
-\fB\-\-homozyg\-window\-threshold\fR [min scanning window hit rate]
-.IP
-These commands request a set of run\-of\-homozygosity reports, and allow you
-to customize how they are generated.
-* If you're satisfied with all the default settings described below, just
-.TP
-use \fB\-\-homozyg\fR with no modifiers.
-Otherwise, \fB\-\-homozyg\fR lets you change a
-.IP
-few binary settings:
-* 'group{\-verbose}' adds a report on pools of overlapping runs of
-.TP
-homozygosity.
-(Automatically set when \fB\-\-homozyg\-match\fR is present.)
-.IP
-* With 'group{\-verbose}', 'consensus\-match' causes pairwise segmental
-.IP
-matches to be called based on the variants in the pool's consensus
-segment, rather than the variants in the pairwise intersection.
-.IP
-* Due to how the scanning window algorithm works, it is possible for a
-.TP
-reported ROH to be adjacent to a few homozygous variants.
-The 'extend'
-.IP
-modifier causes them to be included in the reported ROH if that
-wouldn't cause a violation of the \fB\-\-homozyg\-density\fR bound.
-.IP
-* By default, segment bp lengths are calculated as [end bp position] \-
-.TP
-[start bp position] + 1.
-Therefore, reports normally differ slightly
-.TP
-from PLINK 1.07, which does not add 1 at the end.
-For testing
-.IP
-purposes, you can use the 'subtract\-1\-from\-lengths' modifier to apply
-the old formula.
-.IP
-* By default, only runs of homozygosity containing at least 100 variants,
-.TP
-and of total length >= 1000 kilobases, are noted.
-You can change these
-.IP
-minimums with \fB\-\-homozyg\-snp\fR and \fB\-\-homozyg\-kb\fR, respectively.
-.IP
-* By default, a ROH must have at least one variant per 50 kb on average;
-.IP
-change this bound with \fB\-\-homozyg\-density\fR.
-.IP
-* By default, if two consecutive variants are more than 1000 kb apart, they
-.IP
-cannot be in the same ROH; change this bound with \fB\-\-homozyg\-gap\fR.
-.IP
-* By default, a ROH can contain an unlimited number of heterozygous calls;
-.IP
-you can impose a limit with \fB\-\-homozyg\-het\fR.
-.IP
-* By default, the scanning window contains 50 variants; change this with
-.HP
-\fB\-\-homozyg\-window\-snp\fR.
-.IP
-* By default, a scanning window hit can contain at most 1 heterozygous
-.IP
-call and 5 missing calls; change these limits with \fB\-\-homozyg\-window\-het\fR
-and \fB\-\-homozyg\-window\-missing\fR, respectively.
-.IP
-* By default, for a variant to be eligible for inclusion in a ROH, the hit
-.IP
-rate of all scanning windows containing the variant must be at least
-0.05; change this threshold with \fB\-\-homozyg\-window\-threshold\fR.
-.HP
-\fB\-\-cluster\fR <cc> <group\-avg | old\-tiebreaks> <missing> <only2>
-.IP
-Cluster samples using a pairwise similarity statistic (normally IBS).
-* The 'cc' modifier forces every cluster to have at least one case and one
-.IP
-control.
-.IP
-* The 'group\-avg' modifier causes clusters to be joined based on average
-.IP
-instead of minimum pairwise similarity.
-.IP
-* The 'missing' modifier causes clustering to be based on
-.IP
-identity\-by\-missingness instead of identity\-by\-state, and writes a
-space\-delimited identity\-by\-missingness matrix to disk.
-.IP
-* The 'only2' modifier causes only a .cluster2 file (which is valid input
-.IP
-for \fB\-\-within\fR) to be written; otherwise 2 other files will be produced.
-.IP
-* By default, IBS ties are not broken in the same manner as PLINK 1.07, so
-.TP
-final cluster solutions tend to differ.
-This is generally harmless.
-.IP
-However, to simplify testing, you can use the 'old\-tiebreaks' modifier to
-force emulation of the old algorithm.
-.HP
-\fB\-\-pca\fR {count} <header> <tabs> <var\-wts>
-.IP
-Calculates a variance\-standardized relationship matrix (use \fB\-\-make\-rel\fR or
-\fB\-\-make\-grm\-gz\fR to dump it), and extracts the top 20 principal components.
-* It is usually best to perform this calculation on a marker set in
-.IP
-approximate linkage equilibrium.
-.IP
-* You can change the number of PCs by passing a numeric parameter.
-* The 'header' modifier adds a header line to the .eigenvec output file.
-.IP
-(For compatibility with the GCTA flag of the same name, the default is no
-header line.)
-.IP
-* The 'tabs' modifier causes the .eigenvec file(s) to be tab\-delimited.
-* The 'var\-wts' modifier requests an additional .eigenvec.var file with PCs
-.IP
-expressed as variant weights instead of sample weights.
-.HP
-\fB\-\-neighbour\fR [n1] [n2]
-.IP
-(alias: \fB\-\-neighbor\fR)
-Report IBS distances from each sample to their n1th\- to n2th\-nearest
-neighbors, associated Z\-scores, and the identities of those neighbors.
-Useful for outlier detection.
-.HP
-\fB\-\-assoc\fR <perm | mperm=[value]> <perm\-count> <fisher | fisher\-midp> <counts>
-.IP
-<set\-test>
-.HP
-\fB\-\-assoc\fR <perm | mperm=[value]> <perm\-count> <qt\-means> <lin> <set\-test>
-.HP
-\fB\-\-model\fR <perm | mperm=[value]> <perm\-count>
-.IP
-<fisher | fisher\-midp | trend\-only> <set\-test>
-<dom | rec | gen | trend>
-.IP
-Basic association analysis report.
-Given a case/control phenotype, \fB\-\-assoc\fR performs a 1df chi\-square allelic
-test, while \fB\-\-model\fR performs 4 other tests as well (1df dominant gene
-action, 1df recessive gene action, 2df genotypic, Cochran\-Armitage trend).
-* With 'fisher'/'fisher\-midp', Fisher's exact test is used to generate
-.TP
-p\-values.
-\&'fisher\-midp' also applies Lancaster's mid\-p adjustment.
-.IP
-* 'perm' causes an adaptive permutation test to be performed.
-* 'mperm=[value]' causes a max(T) permutation test with the specified
-.IP
-number of replications to be performed.
-.IP
-* 'perm\-count' causes the permutation test report to include counts instead
-.IP
-of frequencies.
-.IP
-* 'counts' causes \fB\-\-assoc\fR to report allele counts instead of frequencies.
-* 'set\-test' tests the significance of variant sets. Requires permutation;
-.IP
-can be customized with \fB\-\-set\-p\fR/\-\-set\-r2/\-\-set\-max.
-.IP
-* 'dom', 'rec', 'gen', and 'trend' force the corresponding test to be used
-.TP
-as the basis for \fB\-\-model\fR permutation.
-(By default, the most significant
-.IP
-result among the allelic, dominant, and recessive tests is used.)
-.IP
-* 'trend\-only' causes only the trend test to be performed.
-Given a quantitative phenotype, \fB\-\-assoc\fR normally performs a Wald test.
-* In this case, the 'qt\-means' modifier causes trait means and standard
-.IP
-deviations stratified by genotype to be reported as well.
-.IP
-* 'lin' causes the Lin statistic to be computed, and makes it the basis for
-.IP
-multiple\-testing corrections and permutation tests.
-.IP
-Several other flags (most notably, \fB\-\-aperm\fR) can be used to customize the
-permutation test.
-.HP
-\fB\-\-mh\fR <perm | mperm=[value]> <perm\-count> <set\-test>
-.IP
-(alias: \fB\-\-cmh\fR)
-.HP
-\fB\-\-bd\fR <perm | perm\-bd | mperm=[value]> <perm\-count> <set\-test>
-.HP
-\fB\-\-mh2\fR
-.HP
-\fB\-\-homog\fR
-.IP
-Given a case/control phenotype and a set of clusters, \fB\-\-mh\fR computes 2x2xK
-Cochran\-Mantel\-Haenszel statistics for each variant, while \fB\-\-bd\fR also
-performs the Breslow\-Day test for odds ratio homogeneity. Permutation and
-variant set testing based on the CMH (default) or Breslow\-Day (when
-\&'perm\-bd' is present) statistic are supported.
-The following similar analyses are also available:
-* \fB\-\-mh2\fR swaps the roles of case/control status and cluster membership,
-.IP
-performing a phenotype\-stratified IxJxK Cochran\-Mantel\-Haenszel test on
-association between cluster assignments and genotypes.
-.IP
-* \fB\-\-homog\fR executes an alternative to the Breslow\-Day test, based on
-.IP
-partitioning of the chi\-square statistic.
-.HP
-\fB\-\-gxe\fR {covariate index}
-.IP
-Given both a quantitative phenotype and a case/control covariate loaded
-with \fB\-\-covar\fR defining two groups, \fB\-\-gxe\fR compares the regression coefficient
-derived from considering only members of one group to the regression
-coefficient derived from considering only members of the other. By
-default, the first covariate in the \fB\-\-covar\fR file defines the groups; use
-e.g. '\-\-gxe 3' to base them on the third covariate instead.
-.HP
-\fB\-\-linear\fR <perm | mperm=[value]> <perm\-count> <set\-test>
-.IP
-<genotypic | hethom | dominant | recessive | no\-snp> <hide\-covar>
-<sex | no\-x\-sex> <interaction> <beta> <standard\-beta> <intercept>
-.HP
-\fB\-\-logistic\fR <perm | mperm=[value]> <perm\-count> <set\-test>
-.IP
-<genotypic | hethom | dominant | recessive | no\-snp> <hide\-covar>
-<sex | no\-x\-sex> <interaction> <beta>
-.IP
-Multi\-covariate association analysis on a quantitative (\fB\-\-linear\fR) or
-case/control (\fB\-\-logistic\fR) phenotype. Normally used with \fB\-\-covar\fR.
-* 'perm' normally causes an adaptive permutation test to be performed on
-.IP
-the main effect, while 'mperm=[value]' starts a max(T) permutation test.
-.IP
-* 'perm\-count' causes the permutation test report to include counts instead
-.IP
-of frequencies.
-.TP
-* 'set\-test' tests the significance of variant sets.
-Requires permutation;
-.IP
-can be customized with \fB\-\-set\-p\fR/\-\-set\-r2/\-\-set\-max.
-.IP
-* The 'genotypic' modifier adds an additive effect/dominance deviation 2df
-.IP
-joint test (0/1/2 and 0/1/0 coding), while 'hethom' uses 0/0/1 and 0/1/0
-coding instead. If permutation is also requested, these modifiers cause
-permutation to be based on the joint test.
-.IP
-* 'dominant' and 'recessive' specify a model assuming full dominance or
-.IP
-recessiveness, respectively, for the A1 allele.
-.IP
-* 'no\-snp' causes regression to be performed only on the phenotype and the
-.TP
-covariates, without reference to genomic data.
-If permutation is also
-.IP
-requested, results are reported for all covariates.
-.IP
-* 'hide\-covar' removes covariate\-specific lines from the report.
-* By default, sex (male = 1, female = 0) is automatically added as a
-.TP
-covariate on X chromosome variants, and nowhere else.
-The 'sex' modifier
-.IP
-causes it to be added everywhere, while 'no\-x\-sex' excludes it.
-.TP
-* 'interaction' adds genotype x covariate interactions to the model.
-This
-.IP
-cannot be used with the usual permutation tests; use \fB\-\-tests\fR to define
-the permutation test statistic instead.
-.IP
-* For logistic regressions, the 'beta' modifier causes regression
-.IP
-coefficients instead of odds ratios to be reported.
-.IP
-* With \fB\-\-linear\fR, the 'standard\-beta' modifier standardizes the phenotype
-.IP
-and all predictors to zero mean and unit variance before regression, and
-the 'intercept' modifier adds intercepts to the main report.
-.HP
-\fB\-\-dosage\fR [allele dosage file] <noheader> <skip0=[i]> <skip1=[j]> <skip2=[k]>
-.IP
-<dose1> <format=[m]> <Zout> <occur | standard\-beta> <sex>
-.HP
-\fB\-\-dosage\fR [list file] list <sepheader | noheader> <skip0=[i]> <skip1=[j]>
-.IP
-<skip2=[k]> <dose1> <format=[m]> <Zout> <occur | standard\-beta>
-<sex>
-.HP
-\fB\-\-write\-dosage\fR
-.IP
-Process (possibly gzipped) text files with variant\-major allelic dosage
-data. This cannot be used with a regular input fileset; instead, you must
-*only* specify a .fam and possibly a .map file, and you can't specify any
-other commands.
-* PLINK 2.0 will have first\-class support for genotype probabilities. An
-.IP
-equivalent data import flag will be provided then, and \fB\-\-dosage\fR will be
-retired.
-.IP
-* By default, \fB\-\-dosage\fR assumes that only one allelic dosage file should be
-.TP
-loaded.
-To specify multiple files,
-.TP
-1. create a master list with one entry per line.
-There are normally two
-.IP
-supported formats for this list: just a filename per line, or variant
-batch numbers in the first column and filenames in the second.
-.IP
-2. Provide the name of that list as the first \fB\-\-dosage\fR parameter.
-3. Add the 'list' modifier.
-.IP
-* By default, \fB\-\-dosage\fR assumes the allelic dosage file(s) contain a header
-.IP
-line, which has 'SNP' in column i+1, 'A1' in column i+j+2, 'A2' in column
-i+j+3, and sample FID/IIDs starting from column i+j+k+4. (i/j/k are
-normally zero, but can be changed with 'skip0', 'skip1', and 'skip2'
-respectively.) If such a header line is not present,
-* when all samples appear in the same order as they do in the .fam file,
-.IP
-you can use the 'noheader' modiifer.
-.IP
-* Otherwise, use the 'sepheader' modifier, and append sample ID filenames
-.IP
-to your 'list' file entries.
-.IP
-* The 'format' modifier lets you specify the number of values used to
-.TP
-represent each dosage.
-\&'format=1' normally indicates a single 0..2 A1
-.TP
-expected count; 'dose1' modifies this to a 0..1 frequency.
-\&'format=2'
-.IP
-(the default) indicates a 0..1 homozygous A1 likelihood followed by a
-0..1 het likelihood, while 'format=3' indicates 0..1 hom A1, 0..1 het,
-0..1 hom A2.
-.IP
-* 'Zout' causes the output file to be gzipped.
-* Normally, an association analysis is performed. 'standard\-beta' and
-.TP
-\&'sex' behave as they are supposed to with \fB\-\-linear\fR/\-\-logistic.
-(Note
-.IP
-that \fB\-\-dosage\fR + \fB\-\-sex\fR did NOT work properly in PLINK 1.07.)
-.IP
-* There are three alternate modes which cause the association analysis to
-.IP
-be skipped.
-* 'occur' requests a simple variant occurrence report.
-* \fB\-\-write\-dosage\fR causes a simple merged file matching the 'format'
-.IP
-specification (not including 'dose1') to be generated.
-.IP
-* \fB\-\-score\fR applies a linear scoring system to the dosages.
-.HP
-\fB\-\-lasso\fR [h2 estimate] {min lambda} <report\-zeroes>
-.TP
-Estimate variant effect sizes via LASSO regression.
-You must provide an
-.IP
-additive heritability estimate to calibrate the regression.
-Note that this method may require a very large sample size (e.g. hundreds
-of thousands) to be effective on complex polygenic traits.
-.HP
-\fB\-\-test\-missing\fR <perm | mperm=[value]> <perm\-count> <midp>
-.IP
-Check for association between missingness and case/control status, using
-Fisher's exact test. The 'midp' modifier causes Lancaster's mid\-p
-adjustment to be applied.
-.HP
-\fB\-\-make\-perm\-pheno\fR [ct]
-.IP
-Generate phenotype permutations and write them to disk, without invoking an
-association test.
-.HP
-\fB\-\-tdt\fR <exact | exact\-midp | poo> <perm | mperm=[value]>
-.IP
-<parentdt1 | parentdt2 | pat | mat> <set\-test>
-.IP
-Report transmission disequilibrium test statistics, given case/control
-phenotypes and pedigree information.
-* A Mendel error check is performed before the main tests; offending
-.IP
-genotypes are treated as missing by this analysis.
-.IP
-* By default, the basic TDT p\-value is based on a chi\-square test unless
-.IP
-you request the exact binomial test with 'exact' or 'exact\-midp'.
-.IP
-* 'perm'/'mperm=[value]' requests a family\-based adaptive or max(T)
-.TP
-permutation test.
-By default, the permutation test statistic is the
-.IP
-basic TDT p\-value; 'parentdt1'/'parentdt2' cause parenTDT or combined
-test p\-values, respectively, to be considered instead.
-.TP
-* 'set\-test' tests the significance of variant sets.
-This cannot be used
-.IP
-with exact tests for now.
-.IP
-The 'poo' modifier causes a parent\-of\-origin analysis to be performed
-instead, with transmissions from heterozygous fathers and heterozygous
-mothers considered separately.
-* The parent\-of\-origin analysis does not currently support exact tests.
-* By default, the permutation test statistic is the absolute
-.IP
-parent\-of\-origin test Z score; 'pat'/'mat' cause paternal or maternal TDT
-chi\-square statistics, respectively, to be considered instead.
-.HP
-\fB\-\-qfam\fR <perm | mperm=[value]> <perm\-count>
-.HP
-\fB\-\-qfam\-parents\fR <perm | mperm=[value]> <perm\-count>
-.HP
-\fB\-\-qfam\-between\fR <perm | mperm=[value]> <perm\-count>
-.HP
-\fB\-\-qfam\-total\fR <perm | mperm=[value]> <perm\-count>
-.IP
-QFAM family\-based association test for quantitative traits.
-* A Mendel error check is performed before the main tests; offending
-.IP
-genotypes are treated as missing by this analysis.
-.TP
-* This procedure requires permutation.
-\&'perm' and 'perm\-count' have the
-.TP
-usual meanings.
-However, 'mperm=[value]' just specifies a fixed number
-.IP
-of permutations; the method does not support a proper max(T) test.
-.HP
-\fB\-\-annotate\fR [PLINK report] <attrib=[file]> <ranges=[file]> <filter=[file]>
-.IP
-<snps=[file]> <NA | prune> <block> <subset=[file]> <minimal>
-<distance>
-.TP
-Add annotations to a variant\-based PLINK report.
-This requires an
-.IP
-annotation source:
-* 'attrib=[file]' specifies a (possibly gzipped) attribute file.
-* 'ranges=[file]' specifies a gene/range list file.
-(Both source types can be specified simultaneously.) The following options
-are also supported:
-* 'filter=[file]' causes only variants within one of the ranges in the file
-.IP
-to be included in the new report.
-.IP
-* 'snps=[file]' causes only variants named in the file to be included in
-.IP
-the new report.
-.IP
-* The 'NA' modifier causes unannotated variants to have 'NA' instead of '.'
-.IP
-in the new report's ANNOT column, while the 'prune' modifier excludes
-them entirely.
-.IP
-* The 'block' modifier replaces the single ANNOT column with a 0/1\-coded
-.IP
-column for each possible annotation.
-.IP
-* With 'ranges',
-.IP
-* 'subset=[file]' causes only intervals named in the subset file to be
-.IP
-loaded from the ranges file.
-.IP
-* interval annotations normally come with a parenthesized signed distance
-.IP
-to the interval boundary (0 if the variant is located inside the
-interval; this is always true without \fB\-\-border\fR). They can be excluded
-with the 'minimal' modifier.
-.IP
-* the 'distance' modifier adds 'DIST' and 'SGN' columns describing signed
-.IP
-distance to the nearest interval.
-.IP
-* When \fB\-\-pfilter\fR is present, high p\-values are filtered out.
-.HP
-\fB\-\-clump\fR [PLINK report filename(s)...]
-.IP
-Process association analysis report(s) with 'SNP' and p\-value columns,
-organizing results by LD\-based clumps. Multiple filenames can be separated
-by spaces or commas.
-.HP
-\fB\-\-gene\-report\fR [PLINK report] [gene range file]
-.IP
-Generate a gene\-based report from a variant\-based report.
-* When \fB\-\-pfilter\fR is present, high p\-values are filtered out.
-* When \fB\-\-extract\fR (without 'range') is present, only variants named in the
-.HP
-\fB\-\-extract\fR file are considered.
-.HP
-\fB\-\-fast\-epistasis\fR <boost | joint\-effects | no\-ueki> <case\-only>
-.IP
-<set\-by\-set | set\-by\-all> <nop>
-.HP
-\fB\-\-epistasis\fR <set\-by\-set | set\-by\-all>
-.TP
-Scan for epistatic interactions.
-\fB\-\-fast\-epistasis\fR inspects 3x3 joint
-.IP
-genotype count tables and only applies to case/control phenotypes, while
-\fB\-\-epistasis\fR performs linear or logistic regression.
-* By default, \fB\-\-fast\-epistasis\fR uses the PLINK 1.07 allele\-based test. Two
-.IP
-newer tests are now supported: 'boost' invokes the likelihood ratio test
-introduced by Wan X et al. (2010) BOOST: A Fast Approach to Detecting
-Gene\-Gene Interactions in Genome\-wide Case\-Control Studies, while
-\&'joint\-effects' applies the joint effects test introduced in Ueki M,
-Cordell HJ (2012) Improved statistics for genome\-wide interaction
-analysis.
-.IP
-* The original \fB\-\-fast\-epistasis\fR test normally applies the variance and
-.TP
-empty cell corrections suggested by Ueki and Cordell's paper.
-To disable
-.IP
-them, use the 'no\-ueki' modifier.
-.IP
-* 'case\-only' requests a case\-only instead of a case/control test.
-* By default, all pairs of variants across the entire genome are tested.
-.IP
-To just test pairs of variants within a single set, add the 'set\-by\-set'
-modifier and load exactly one set with \fB\-\-set\fR/\-\-make\-set; with exactly two
-sets loaded, all variants in one set are tested against all variants in
-the other. 'set\-by\-all' tests all variants in one set against the entire
-genome instead.
-.IP
-* 'nop' strips p\-values from the main report.
-* These computations can be subdivided with \fB\-\-parallel\fR; however...
-.HP
-\fB\-\-epistasis\-summary\-merge\fR [common file prefix] [ct]
-.IP
-When a \fB\-\-\fR{fast\-}epistasis job is subdivided with \fB\-\-parallel\fR, the main
-report can be assembled at the end by applying Unix 'cat' in the usual
-manner, but the .summary.1, .summary.2, ... files may require a specialized
-merge. \fB\-\-epistasis\-summary\-merge\fR takes care of the latter.
-.HP
-\fB\-\-twolocus\fR [variant ID] [variant ID]
-.IP
-Two\-locus joint genotype count report.
-.HP
-\fB\-\-score\fR [filename] {i} {j} {k} <header> <sum | no\-sum>
-.IP
-<no\-mean\-imputation | center> <include\-cnt>
-.IP
-Apply a linear scoring system to each sample.
-The input file should have one line per scored variant. Variant IDs are
-read from column #i, allele codes are read from column #j, and scores are
-read from column #k, where i defaults to 1, j defaults to i+1, and k
-defaults to j+1.
-* The 'header' modifier causes the first nonempty line of the input file to
-.IP
-be ignored; otherwise, \fB\-\-score\fR assumes there is no header line.
-.IP
-* By default, final scores are averages of the valid per\-variant scores.
-.TP
-The 'sum' modifier causes sums to be reported instead.
-(This cannot be
-.TP
-used with 'no\-mean\-imputation'.
-And for backward compatibility, 'sum' is
-.IP
-automatically on with dosage data unless 'no\-sum' is specified.)
-.IP
-* By default, copies of the unnamed allele contribute zero to score, while
-.IP
-missing genotypes contribute an amount proportional to the loaded (via
-\fB\-\-read\-freq\fR) or imputed allele frequency. To throw out missing
-observations instead (decreasing the denominator in the final average
-when this happens), use the 'no\-mean\-imputation' modifier.
-.IP
-* Alternatively, you can use the 'center' modifier to shift all scores to
-.IP
-mean zero.
-.TP
-* This command can be used with dosage data.
-By default, the 'CNT' column
-.IP
-is omitted from the output file in this case; use 'include\-cnt' to keep
-it.
-.HP
-\fB\-\-write\-var\-ranges\fR [block ct]
-.TP
-Divide the set of variants into equal\-size blocks.
-(Can be used with
-.HP
-\fB\-\-snps\fR to split a job across multiple machines.)
-.PP
-The following other flags are supported. (Order of operations is described at
-https://www.cog\-genomics.org/plink2/order .)
-.HP
-\fB\-\-script\fR [fname] : Include command\-line options from file.
-.TP
-\fB\-\-rerun\fR {log}
-: Rerun commands in log (default 'plink.log').
-.TP
-\fB\-\-version\fR
-: Display only version number before exiting.
-.TP
-\fB\-\-silent\fR
-: Suppress output to console.
-.TP
-\fB\-\-gplink\fR
-: Reserved for interoperation with gPLINK.
-.HP
-\fB\-\-missing\-genotype\fR [char] : Set missing genotype code (normally '0').
-.TP
-\fB\-\-double\-id\fR
-: Set both FIDs and IIDs to the VCF/BCF sample ID.
-.TP
-\fB\-\-const\-fid\fR {ID}
-: Set all FIDs to the given constant (default '0').
-.TP
-\fB\-\-id\-delim\fR {d}
-: Parse sample IDs as [FID][d][IID] (default delim '_').
-.HP
-\fB\-\-vcf\-idspace\-to\fR [c] : Convert spaces in sample IDs to the given character.
-.HP
-\fB\-\-biallelic\-only\fR <strict> <list> : Skip VCF variants with 2+ alt. alleles.
-.TP
-\fB\-\-vcf\-min\-qual\fR [val]
-: Skip VCF variants with low/missing QUAL.
-.TP
-\fB\-\-vcf\-filter\fR {exception(s)...}
-: Skip variants which have FILTER failures.
-.TP
-\fB\-\-vcf\-half\-call\fR [m]
-: Specify how '0/.' and similar VCF GT values should be
-handled. The following three modes are supported:
-* 'error'/'e' (default) errors out and reports line #.
-* 'haploid'/'h' treats them as haploid calls.
-* 'missing'/'m' treats them as missing.
-.TP
-\fB\-\-oxford\-single\-chr\fR [chr nm] : Specify single\-chromosome .gen file with
-ignorable first column.
-.HP
-\fB\-\-oxford\-pheno\-name\fR [col nm] : Import named phenotype from the .sample file.
-.TP
-\fB\-\-hard\-call\-threshold\fR [val]
-: When an Oxford\-format fileset is loaded, calls
-.TP
-\fB\-\-hard\-call\-threshold\fR random
-with uncertainty level greater than 0.1 are
-normally treated as missing. You can adjust
-this threshold by providing a numeric
-parameter, or randomize all calls with
-\&'random'.
-.HP
-\fB\-\-missing\-code\fR {string list} : Comma\-delimited list of missing phenotype
-.TP
-(alias: \fB\-\-missing_code\fR)
-values for Oxford\-format filesets (def. 'NA').
-.TP
-\fB\-\-simulate\-ncases\fR [num]
-: Set \fB\-\-simulate\fR case count (default 1000).
-.TP
-\fB\-\-simulate\-ncontrols\fR [n]
-: Set \fB\-\-simulate\fR control count (default 1000).
-.HP
-\fB\-\-simulate\-prevalence\fR [p] : Set \fB\-\-simulate\fR disease prevalence (default 0.01).
-.TP
-\fB\-\-simulate\-n\fR [num]
-: Set \fB\-\-simulate\-qt\fR sample count (default 1000).
-.HP
-\fB\-\-simulate\-label\fR [prefix] : Set \fB\-\-simulate\fR{\-qt} FID/IID name prefix.
-.HP
-\fB\-\-simulate\-missing\fR [freq] : Set \fB\-\-simulate\fR{\-qt} missing genotype frequency.
-.TP
-\fB\-\-allow\-extra\-chr\fR <0>
-: Permit unrecognized chromosome codes. The '0'
-.TP
-(alias: \fB\-\-aec\fR)
-modifier causes them to be treated as if they had
-been set to zero.
-.HP
-\fB\-\-chr\-set\fR [autosome ct] <no\-x> <no\-y> <no\-xy> <no\-mt> :
-.TP
-Specify a nonhuman chromosome set.
-The first parameter sets the number of
-.IP
-diploid autosome pairs if positive, or haploid chromosomes if negative.
-Given diploid autosomes, the remaining modifiers indicate the absence of
-the named non\-autosomal chromosomes.
-.HP
-\fB\-\-cow\fR/\-\-dog/\-\-horse/\-\-mouse/\-\-rice/\-\-sheep : Shortcuts for those species.
-.TP
-\fB\-\-autosome\-num\fR [value]
-: Alias for '\-\-chr\-set [value] no\-y no\-xy no\-mt'.
-.TP
-\fB\-\-cm\-map\fR [fname pattern] {chr} : Use SHAPEIT\-format recombination maps to set
-centimorgan positions. To process more than
-one chromosome, include a '@' in the first
-parameter where the chrom. number belongs,
-e.g. 'genetic_map_chr at _combined_b37.txt'.
-.TP
-\fB\-\-zero\-cms\fR
-: Zero out centimorgan positions.
-.TP
-\fB\-\-pheno\fR [fname]
-: Load phenotype data from the specified file, instead of
-using the values in the main input fileset.
-.TP
-\fB\-\-all\-pheno\fR
-: For basic association tests, loop through all phenotypes
-in \fB\-\-pheno\fR file.
-.TP
-\fB\-\-mpheno\fR [col]
-: Specify phenotype column number in \fB\-\-pheno\fR file.
-.TP
-\fB\-\-pheno\-name\fR [c] : If \fB\-\-pheno\fR file has a header row, use column with the
-given name.
-.TP
-\fB\-\-pheno\-merge\fR
-: When the main input fileset contains an phenotype value
-for a sample, but the \fB\-\-pheno\fR file does not, use the
-original value instead of treating the phenotype as
-missing.
-.HP
-\fB\-\-missing\-phenotype\fR [v] : Set missing phenotype value (normally \fB\-9\fR).
-.TP
-\fB\-\-1\fR
-: Expect case/control phenotypes to be coded as
-0 = control, 1 = case, instead of the usual
-0 = missing, 1 = control, 2 = case.
-.TP
-\fB\-\-make\-pheno\fR [fn] [val] : Define a new case/control phenotype.
-If the val
-parameter is '*', all samples listed in the given
-file are cases, and everyone else is a control.
-(Note that, in some shells, it is necessary to
-surround the * with quotes.)
-Otherwise, all samples with third column entry
-equal to the val parameter are cases, and all other
-samples mentioned in the file are controls.
-.TP
-\fB\-\-tail\-pheno\fR [Lt] {Hbt} : Downcode a scalar phenotype to a case/control
-phenotype. All samples with phenotype values
-greater than Hbt are cases, and all with values
-less than or equal to Lt are controls. If Hbt is
-unspecified, it is equal to Lt; otherwise,
-in\-between phenotype values are set to missing.
-.HP
-\fB\-\-covar\fR [filename] <keep\-pheno\-on\-missing\-cov> : Specify covariate file.
-.TP
-\fB\-\-covar\-name\fR [...]
-: Specify covariate(s) in \fB\-\-covar\fR file by name.
-Separate multiple names with spaces or commas, and
-use dashes to designate ranges.
-.TP
-\fB\-\-covar\-number\fR [...]
-: Specify covariate(s) in \fB\-\-covar\fR file by index.
-.TP
-\fB\-\-within\fR [f] <keep\-NA>
-: Specify initial cluster assignments.
-.TP
-\fB\-\-mwithin\fR [n]
-: Load cluster assignments from column n+2.
-.TP
-\fB\-\-family\fR
-: Create a cluster for each family ID.
-.TP
-\fB\-\-loop\-assoc\fR [f] <keep\-NA>
-: Run specified case/control association
-commands once for each cluster in the file,
-using cluster membership as the phenotype.
-.TP
-\fB\-\-set\fR [filename]
-: Load sets from a .set file.
-.TP
-\fB\-\-set\-names\fR [name(s)...]
-: Load only sets named on the command line.
-Use spaces to separate multiple names.
-.TP
-\fB\-\-subset\fR [filename]
-: Load only sets named in the given text file.
-.HP
-\fB\-\-set\-collapse\-all\fR [set name] : Merge all sets.
-.TP
-\fB\-\-complement\-sets\fR
-: Invert all sets. (Names gain 'C_' prefixes.)
-.HP
-\fB\-\-make\-set\-complement\-all\fR [s] : \fB\-\-set\-collapse\-all\fR + inversion.
-.TP
-\fB\-\-make\-set\fR [filename]
-: Define sets from a list of named bp ranges.
-.TP
-\fB\-\-make\-set\-border\fR [kbs]
-: Stretch regions in \fB\-\-make\-set\fR file.
-.TP
-\fB\-\-make\-set\-collapse\-group\fR
-: Define sets from groups instead of sets in
-\fB\-\-make\-set\fR file.
-.TP
-\fB\-\-keep\fR [filename]
-: Exclude all samples not named in the file.
-.TP
-\fB\-\-remove\fR [filename]
-: Exclude all samples named in the file.
-.HP
-\fB\-\-keep\-fam\fR [filename] : Exclude all families not named in the file.
-.TP
-\fB\-\-remove\-fam\fR [fname]
-: Exclude all families named in the file.
-.HP
-\fB\-\-extract\fR <range> [f] : Exclude all variants not named in the file.
-.HP
-\fB\-\-exclude\fR <range> [f] : Exclude all variants named in the file.
-.TP
-\fB\-\-keep\-clusters\fR [filename]
-: These can be used individually or in
-.TP
-\fB\-\-keep\-cluster\-names\fR [name(s)...]
-combination to define a list of
-clusters to keep; all samples not in a
-cluster in that list are then excluded.
-Use spaces to separate cluster names
-for \fB\-\-keep\-cluster\-names\fR.
-.TP
-\fB\-\-remove\-clusters\fR [filename]
-: Exclude all clusters named in the file.
-.HP
-\fB\-\-remove\-cluster\-names\fR [name(s)...] : Exclude the named clusters.
-.TP
-\fB\-\-gene\fR [sets...] : Exclude variants not in a set named on the command line.
-(Separate multiple set names with spaces.)
-.TP
-\fB\-\-gene\-all\fR
-: Exclude variants which aren't a member of any set. (PLINK
-1.07 automatically did this under some circumstances.)
-.HP
-\fB\-\-attrib\fR [f] {att lst} : Given a file assigning attributes to variants, and a
-.TP
-\fB\-\-attrib\-indiv\fR [f] {a}
-comma\-delimited list (with no whitespace) of
-attribute names, remove variants/samples which are
-either missing from the file or don't have any of
-the listed attributes. If some attribute names in
-the list are preceded by '\-', they are treated as
-\&'negative match conditions' instead: variants with
-all the negative match attributes are removed.
-The first character in the list cannot be a '\-', due
-to how command\-line parsing works; add a comma in
-front to get around this.
-.TP
-\fB\-\-chr\fR [chrs...]
-: Exclude all variants not on the given chromosome(s).
-Valid choices for humans are 0 (unplaced), 1\-22, X, Y, XY,
-and MT. Separate multiple chromosomes with spaces and/or
-commas, and use a dash (no adjacent spaces permitted) to
-denote a range, e.g. '\-\-chr 1\-4, 22, xy'.
-.TP
-\fB\-\-not\-chr\fR [...]
-: Reverse of \fB\-\-chr\fR (exclude variants on listed chromosomes).
-.TP
-\fB\-\-autosome\fR
-: Exclude all non\-autosomal variants.
-.TP
-\fB\-\-autosome\-xy\fR
-: Exclude all non\-autosomal variants, except those with
-chromosome code XY (pseudo\-autosomal region of X).
-.HP
-\fB\-\-snps\-only\fR <no\-DI> : Exclude variants with multi\-character allele codes.
-.TP
-\fB\-\-from\fR [var ID]
-: Use ID(s) to specify a variant range to load. When used
-.TP
-\fB\-\-to\fR
-[var ID] together, both variants must be on the same chromosome.
-.TP
-\fB\-\-snp\fR
-[var ID] : Specify a single variant to load.
-.HP
-\fB\-\-exclude\-snp\fR [] : Specify a single variant to exclude.
-.TP
-\fB\-\-window\fR
-[kbs] : With \fB\-\-snp\fR or \fB\-\-exclude\-snp\fR, loads/excludes all variants
-within half the specified kb distance of the named one.
-.TP
-\fB\-\-from\-bp\fR [pos]
-: Use physical position(s) to define a variant range to
-.TP
-\fB\-\-to\-bp\fR
-[pos] load. \fB\-\-from\-kb\fR/\-\-to\-kb/\-\-from\-mb/\-\-to\-mb allow decimal
-.TP
-\fB\-\-from\-kb\fR [pos]
-values. You must also specify a single chromosome (using
-.TP
-\fB\-\-to\-kb\fR
-[pos] e.g. \fB\-\-chr\fR) when using these flags.
-.HP
-\fB\-\-from\-mb\fR [pos]
-.TP
-\fB\-\-to\-mb\fR
-[pos]
-.TP
-\fB\-\-snps\fR [var IDs...]
-: Use IDs to specify variant range(s) to load or
-.TP
-\fB\-\-exclude\-snps\fR [...]
-exclude. E.g. '\-\-snps rs1111\-rs2222, rs3333, rs4444'.
-.TP
-\fB\-\-thin\fR [p]
-: Randomly remove variants, retaining each with prob. p.
-.HP
-\fB\-\-thin\-count\fR [n] : Randomly remove variants until n of them remain.
-.TP
-\fB\-\-bp\-space\fR [bps] : Remove variants so that each pair is no closer than the
-given bp distance. (Equivalent to VCFtools \fB\-\-thin\fR.)
-.TP
-\fB\-\-filter\fR [f] [val(s)...] : Exclude all samples without a 3rd column entry in
-the given file matching one of the given
-space\-separated value(s).
-.TP
-\fB\-\-mfilter\fR [n]
-: Match against (n+2)th column instead.
-.TP
-\fB\-\-geno\fR {val}
-: Exclude variants with missing call frequencies greater
-than a threshold (default 0.1). (Note that the default
-threshold is only applied if \fB\-\-geno\fR is invoked without a
-parameter; when \fB\-\-geno\fR is not invoked, no per\-variant
-missing call frequency ceiling is enforced at all. Other
-inclusion/exclusion default thresholds work the same way.)
-.TP
-\fB\-\-mind\fR {val}
-: Exclude samples with missing call frequencies greater than
-a threshold (default 0.1).
-.TP
-\fB\-\-oblig\-missing\fR [f1] [f2] : Specify blocks of missing genotype calls for
-\fB\-\-geno\fR/\-\-mind to ignore. The first file should
-have variant IDs in the first column and block
-IDs in the second, while the second file should
-have FIDs in the first column, IIDs in the
-second, and block IDs in the third.
-.TP
-\fB\-\-prune\fR
-: Remove samples with missing phenotypes.
-.TP
-\fB\-\-maf\fR {val}
-: Exclude variants with minor allele frequency lower than a
-threshold (default 0.01).
-.TP
-\fB\-\-max\-maf\fR [val]
-: Exclude variants with MAF greater than the threshold.
-.TP
-\fB\-\-maf\-succ\fR
-: Rule of succession MAF estimation (used in EIGENSOFT).
-Given j observations of one allele and k >= j observations
-of the other, infer a MAF of (j+1) / (j+k+2), rather than
-the default j / (j+k).
-.TP
-\fB\-\-read\-freq\fR [fn] : Estimate MAFs and heterozygote frequencies from the given
-\fB\-\-freq\fR{x} report, instead of the input fileset.
-.TP
-\fB\-\-hwe\fR [p] <midp> <include\-nonctrl> : Exclude variants with Hardy\-Weinberg
-equilibrium exact test p\-values below a
-threshold.
-.TP
-\fB\-\-me\fR [t] [v] <var\-first> : Filter out trios and variants with Mendel error
-rates exceeding the given thresholds.
-.HP
-\fB\-\-me\-exclude\-one\fR {ratio} : Make \fB\-\-me\fR exclude only one sample per trio.
-.TP
-\fB\-\-qual\-scores\fR [f] {qcol} {IDcol} {skip} : Filter out variants with
-out\-of\-range quality scores.
-Default range is now [0, \einfty ).
-.TP
-\fB\-\-qual\-threshold\fR [min qual score]
-: Set \fB\-\-qual\-scores\fR range floor.
-.TP
-\fB\-\-qual\-max\-threshold\fR [max qual score]
-: Set \fB\-\-qual\-scores\fR range ceiling.
-.TP
-\fB\-\-allow\-no\-sex\fR
-: Do not treat ambiguous\-sex samples as having missing
-phenotypes in analysis commands. (Automatic /w \fB\-\-no\-sex\fR.)
-.TP
-\fB\-\-must\-have\-sex\fR
-: Force ambiguous\-sex phenotypes to missing on
-\fB\-\-make\-bed\fR/\-\-make\-just\-fam/\-\-recode/\-\-write\-covar.
-.TP
-\fB\-\-filter\-cases\fR
-: Include only cases in the current analysis.
-.TP
-\fB\-\-filter\-controls\fR
-: Include only controls.
-.TP
-\fB\-\-filter\-males\fR
-: Include only males.
-.TP
-\fB\-\-filter\-females\fR
-: Include only females.
-.TP
-\fB\-\-filter\-founders\fR
-: Include only founders.
-.HP
-\fB\-\-filter\-nonfounders\fR : Include only nonfounders.
-.TP
-\fB\-\-nonfounders\fR
-: Include nonfounders in allele freq/HWE calculations.
-.TP
-\fB\-\-make\-founders\fR <require\-2\-missing> <first> : Clear parental IDs for those
-with 1+ missing parent(s).
-.TP
-\fB\-\-recode\-allele\fR [fn] : With \fB\-\-recode\fR A/A\-transpose/AD, count alleles named in
-the file (otherwise A1 alleles are always counted).
-.TP
-\fB\-\-output\-chr\fR [MT code] : Set chromosome coding scheme in output files by
-providing the desired human mitochondrial code.
-(Options are '26', 'M', 'MT', '0M', 'chr26', 'chrM',
-and 'chrMT'.)
-.TP
-\fB\-\-output\-missing\-genotype\fR [ch] : Set the code used to represent missing
-genotypes in output files (normally the
-\fB\-\-missing\-genotype\fR value).
-.TP
-\fB\-\-output\-missing\-phenotype\fR [s] : Set the string used to represent missing
-phenotypes in output files (normally the
-\fB\-\-missing\-phenotype\fR value).
-.TP
-\fB\-\-zero\-cluster\fR [f] : In combination with \fB\-\-within\fR/\-\-family, set blocks of
-genotype calls to missing. The input file should have
-variant IDs in the first column and cluster IDs in the
-second. This must now be used with \fB\-\-make\-bed\fR and no
-other output commands.
-.TP
-\fB\-\-set\-hh\-missing\fR : Cause \fB\-\-make\-bed\fR and \fB\-\-recode\fR to set heterozygous haploid
-genotypes to missing.
-.HP
-\fB\-\-split\-x\fR [bp1] [bp2] <no\-fail> : Changes chromosome code of all X chromosome
-.TP
-\fB\-\-split\-x\fR [build] <no\-fail>
-variants with bp position <= bp1 or >= bp2
-to XY. The following build codes are
-supported as shorthand:
-* 'b36'/'hg18' = NCBI 36, 2709521/154584237
-* 'b37'/'hg19' = GRCh37, 2699520/154931044
-* 'b38'/'hg38' = GRCh38, 2781479/155701383
-By default, PLINK errors out when no
-variants would be affected by \fB\-\-split\-x\fR;
-the 'no\-fail' modifier (useful in scripts)
-overrides this.
-.TP
-\fB\-\-merge\-x\fR <no\-fail>
-: Merge XY chromosome back with X.
-.TP
-\fB\-\-set\-me\-missing\fR
-: Cause \fB\-\-make\-bed\fR to set Mendel errors to missing.
-.TP
-\fB\-\-fill\-missing\-a2\fR : Cause \fB\-\-make\-bed\fR to replace all missing calls with
-homozygous A2 calls.
-.TP
-\fB\-\-set\-missing\-var\-ids\fR [t]
-: Given a template string with a '@' where the
-chromosome code should go and '#' where the bp
-coordinate belongs, \fB\-\-set\-missing\-var\-ids\fR
-assigns chromosome\-and\-bp\-based IDs to unnamed
-variants.
-You may also use '$1' and '$2' to refer to
-allele names in the template string, and in
-fact this becomes essential when multiple
-variants share the same coordinate.
-.TP
-\fB\-\-new\-id\-max\-allele\-len\fR [n] : Specify maximum number of leading characters
-from allele names to include in new variant IDs
-(default 23).
-.HP
-\fB\-\-missing\-var\-code\fR [string] : Change unnamed variant code (default '.').
-.TP
-\fB\-\-update\-chr\fR
-[f] {chrcol} {IDcol} {skip} : Update variant chromosome codes.
-.TP
-\fB\-\-update\-cm\fR
-[f] {cmcol} {IDcol} {skip} : Update centimorgan positions.
-.TP
-\fB\-\-update\-map\fR
-[f] {bpcol} {IDcol} {skip} : Update variant bp positions.
-.HP
-\fB\-\-update\-name\fR [f] {newcol} {oldcol} {skip} : Update variant IDs.
-.HP
-\fB\-\-update\-alleles\fR [fname] : Update variant allele codes.
-.TP
-\fB\-\-allele1234\fR <multichar> : Interpret/recode A/C/G/T alleles as 1/2/3/4.
-With 'multichar', converts all A/C/G/Ts in allele
-names to 1/2/3/4s.
-.HP
-\fB\-\-alleleACGT\fR <multichar> : Reverse of \fB\-\-allele1234\fR.
-.TP
-\fB\-\-update\-ids\fR [f]
-: Update sample IDs.
-.HP
-\fB\-\-update\-parents\fR [f] : Update parental IDs.
-.TP
-\fB\-\-update\-sex\fR [f] {n} : Update sexes.
-Sex (1 or M = male, 2 or F = female, 0
-= missing) is loaded from column n+2 (default n is 1).
-.TP
-\fB\-\-flip\fR [filename]
-: Flip alleles (A<\->T, C<\->G) for SNP IDs in the file.
-.TP
-\fB\-\-flip\-subset\fR [fn]
-: Only apply \fB\-\-flip\fR to samples in \fB\-\-flip\-subset\fR file.
-.HP
-\fB\-\-flip\-scan\-window\fR [ct+1] : Set \fB\-\-flip\-scan\fR max variant ct dist. (def. 10).
-.HP
-\fB\-\-flip\-scan\-window\-kb\fR [x] : Set \fB\-\-flip\-scan\fR max kb distance (default 1000).
-.HP
-\fB\-\-flip\-scan\-threshold\fR [x] : Set \fB\-\-flip\-scan\fR min correlation (default 0.5).
-.TP
-\fB\-\-keep\-allele\-order\fR
-: Keep the allele order defined in the .bim file,
-instead of forcing A2 to be the major allele.
-.HP
-\fB\-\-a1\-allele\fR [f] {a1col} {IDcol} {skip} : Force alleles in the file to A1.
-.HP
-\fB\-\-a2\-allele\fR [f] {a2col} {IDcol} {skip} : Force alleles in the file to A2.
-.TP
-\fB\-\-indiv\-sort\fR [m] {f} : Specify FID/IID sort order.
-The following four modes
-are supported:
-* 'none'/'0' keeps samples in the order they were
-.TP
-loaded.
-Default for non\-merge operations.
-.IP
-* 'natural'/'n' invokes 'natural sort', e.g.
-.TP
-\&'id2' < 'ID3' < 'id10'.
-Default when merging.
-.IP
-* 'ascii'/'a' sorts in ASCII order, e.g.
-.IP
-\&'ID3' < 'id10' < 'id2'.
-.IP
-* 'file'/'f' uses the order in the given file (named
-.IP
-in the second parameter).
-.IP
-For now, only \fB\-\-merge\fR/\-\-bmerge/\-\-merge\-list and
-\fB\-\-make\-bed\fR/\-\-make\-just\-fam respect this flag.
-.TP
-\fB\-\-with\-phenotype\fR <no\-parents> <no\-sex | female\-2> : Include more sample info
-in new .cov file.
-.TP
-\fB\-\-dummy\-coding\fR {N} <no\-round> : Split categorical variables (n categories,
-2 < n <= N, default N is 49) into n\-1 binary
-dummy variables when writing covariate file.
-.TP
-\fB\-\-merge\-mode\fR [n]
-: Adjust \fB\-\-\fR{b}merge/\-\-merge\-list behavior based on a
-numeric code.
-1 (default) = ignore missing calls, otherwise difference
-.IP
-\-> missing
-.IP
-2 = only overwrite originally missing calls
-3 = only overwrite when nonmissing in new file
-4/5 = never overwrite and always overwrite, respectively
-6 = report all mismatching calls without merging
-7 = report mismatching nonmissing calls without merging
-.TP
-\fB\-\-merge\-equal\-pos\fR
-: Merge variants with different names but identical
-positions.
-.TP
-\fB\-\-mendel\-duos\fR
-: Make Mendel error checks consider samples with only one
-parent in the dataset.
-.TP
-\fB\-\-mendel\-multigen\fR
-: Make Mendel error checks consider (great\-)grandparental
-genotypes when parental genotype data is missing.
-.HP
-\fB\-\-ld\-window\fR [ct+1] : Set \fB\-\-r\fR/\-\-r2 max variant ct pairwise distance (usu. 10).
-.HP
-\fB\-\-ld\-window\-kb\fR [x] : Set \fB\-\-r\fR/\-\-r2 max kb pairwise distance (usually 1000).
-.HP
-\fB\-\-ld\-window\-r2\fR [x] : Set threshold for \fB\-\-r2\fR report inclusion (usually 0.2).
-.TP
-\fB\-\-ld\-snp\fR [var ID]
-: Set first variant in all \fB\-\-r\fR/\-\-r2 pairs.
-.HP
-\fB\-\-ld\-snps\fR [vID...] : Restrict first \fB\-\-r\fR/\-\-r2 variant to the given ranges.
-.TP
-\fB\-\-ld\-snp\-list\fR [f]
-: Restrict first \fB\-\-r\fR/\-\-r2 var. to those named in the file.
-.TP
-\fB\-\-ld\-xchr\fR [code]
-: Set Xchr model for \fB\-\-indep\fR{\-pairwise}, \fB\-\-r\fR/\-\-r2,
-\fB\-\-flip\-scan\fR, and \fB\-\-show\-tags\fR.
-1 (default) = males coded 0/1, females 0/1/2 (A1 dosage)
-2 = males coded 0/2
-3 = males coded 0/2, but females given double weighting
-.TP
-\fB\-\-blocks\-max\-kb\fR [kbs]
-: Set \fB\-\-blocks\fR maximum haploblock span (def. 200).
-.TP
-\fB\-\-blocks\-min\-maf\fR [cutoff]
-: Adjust \fB\-\-blocks\fR MAF minimum (default 0.05).
-.TP
-\fB\-\-blocks\-strong\-lowci\fR [x]
-: Set \fB\-\-blocks\fR 'strong LD' CI thresholds (defaults
-.TP
-\fB\-\-blocks\-strong\-highci\fR [x]
-0.70 and 0.98).
-.HP
-\fB\-\-blocks\-recomb\-highci\fR [x] : Set 'recombination' CI threshold (default 0.90).
-.TP
-\fB\-\-blocks\-inform\-frac\fR [x]
-: Force haploblock [strong LD pairs]:[total
-informative pairs] ratios to be larger than this
-value (default 0.95).
-.TP
-\fB\-\-distance\-exp\fR [x] : When computing genomic distances, assign each variant a
-weight of (2q(1\-q))^{\-x}, where q is the inferred MAF.
-(Use \fB\-\-read\-freq\fR if you want to explicitly specify some
-or all of the MAFs.)
-.TP
-\fB\-\-read\-dists\fR [dist file] {id file} : Load a triangular binary distance matrix
-instead of recalculating from scratch.
-.TP
-\fB\-\-ppc\-gap\fR [val]
-: Minimum number of base pairs, in thousands, between
-informative pairs of markers used in \fB\-\-genome\fR PPC test.
-500 if unspecified.
-.TP
-\fB\-\-min\fR [cutoff]
-: Specify minimum PI_HAT for inclusion in \fB\-\-genome\fR report.
-.TP
-\fB\-\-max\fR [cutoff]
-: Specify maximum PI_HAT for inclusion in \fB\-\-genome\fR report.
-.TP
-\fB\-\-homozyg\-match\fR [] : Set minimum concordance across jointly homozygous
-variants for a pairwise allelic match to be declared.
-.TP
-\fB\-\-pool\-size\fR [ct]
-: Set minimum size of pools in '\-\-homozyg group' report.
-.TP
-\fB\-\-read\-genome\fR [fn] : Load \fB\-\-genome\fR report for \fB\-\-cluster\fR/\-\-neighbour, instead
-of recalculating IBS and PPC test p\-values from scratch.
-.TP
-\fB\-\-ppc\fR [p\-val]
-: Specify minimum PPC test p\-value within a cluster.
-.TP
-\fB\-\-mc\fR [max size]
-: Specify maximum cluster size.
-.TP
-\fB\-\-mcc\fR [c1] [c2]
-: Specify maximum case and control counts per cluster.
-.TP
-\fB\-\-K\fR [min count]
-: Specify minimum cluster count.
-.TP
-\fB\-\-ibm\fR [val]
-: Specify minimum identity\-by\-missingness.
-.TP
-\fB\-\-match\fR [f] {mv} : Use covariate values to restrict clustering.
-Without
-\fB\-\-match\-type\fR, two samples can only be in the same cluster
-if all covariates match. The optional second parameter
-specifies a covariate value to treat as missing.
-.TP
-\fB\-\-match\-type\fR [f] : Refine interpretation of \fB\-\-match\fR file.
-The \fB\-\-match\-type\fR
-file is expected to be a single line with as many entries
-as the \fB\-\-match\fR file has covariates; '0' entries specify
-\&'negative matches' (i.e. samples with equal covariate
-values cannot be in the same cluster), '1' entries specify
-\&'positive matches' (default), and '\-1' causes the
-corresponding covariate to be ignored.
-.HP
-\fB\-\-qmatch\fR [f] {m} : Force all members of a cluster to have similar
-.TP
-\fB\-\-qt\fR [fname]
-quantitative covariate values. The \fB\-\-qmatch\fR file contains
-the covariate values, while the \fB\-\-qt\fR file is a list of
-nonnegative tolerances (and '\-1's marking covariates to
-skip).
-.HP
-\fB\-\-pca\-cluster\-names\fR [...] : These can be used individually or in combination
-.TP
-\fB\-\-pca\-clusters\fR [fname]
-to define a list of clusters to use in the basic
-\fB\-\-pca\fR computation. (\fB\-\-pca\-cluster\-names\fR expects
-a space\-delimited sequence of cluster names,
-while \fB\-\-pca\-clusters\fR expects a file with one
-cluster name per line.) All samples outside
-those clusters will then be projected on to the
-calculated PCs.
-.TP
-\fB\-\-mds\-plot\fR [dims] <by\-cluster> <eigvals> : Multidimensional scaling analysis.
-Requires \fB\-\-cluster\fR.
-.TP
-\fB\-\-cell\fR [thresh]
-: Skip some \fB\-\-model\fR tests when a contingency table entry is
-smaller than the given threshold.
-.TP
-\fB\-\-condition\fR [var ID] <dominant | recessive> : Add one variant as a \fB\-\-linear\fR
-or \fB\-\-logistic\fR covariate.
-.TP
-\fB\-\-condition\-list\fR [f] <dominant | recessive> : Add variants named in the file
-as \fB\-\-linear\fR/\-\-logistic covs.
-.TP
-\fB\-\-parameters\fR [...]
-: Include only the given covariates/interactions in the
-\fB\-\-linear\fR/\-\-logistic models, identified by a list of
-1\-based indices and/or ranges of them.
-.TP
-\fB\-\-tests\fR <all> {...} : Perform a (joint) test on the specified term(s) in the
-\fB\-\-linear\fR/\-\-logistic model, identified by 1\-based
-indices and/or ranges of them. If permutation was
-requested, it is based on this test.
-* Note that, when \fB\-\-parameters\fR is also present, the
-.IP
-indices refer to the terms remaining AFTER pruning by
-\fB\-\-parameters\fR.
-.IP
-* You can use '\-\-tests all' to include all terms.
-.TP
-\fB\-\-vif\fR [max VIF]
-: Set VIF threshold for \fB\-\-linear\fR multicollinearity check
-(default 50).
-.TP
-\fB\-\-xchr\-model\fR [code] : Set the X chromosome \fB\-\-linear\fR/\-\-logistic model.
-0 = skip sex and haploid chromosomes
-1 (default) = add sex as a covariate on X chromosome
-2 = code male genotypes 0/2 instead of 0/1
-3 = test for interaction between genotype and sex
-.TP
-\fB\-\-lasso\-select\-covars\fR {cov(s)...} : Subject some or all covariates to LASSO
-model selection.
-.TP
-\fB\-\-adjust\fR <gc> <log10> <qq\-plot>
-: Report some multiple\-testing corrections.
-.TP
-\fB\-\-lambda\fR [val]
-: Set genomic control lambda for \fB\-\-adjust\fR.
-.TP
-\fB\-\-ci\fR [size]
-: Report confidence intervals for odds ratios.
-.TP
-\fB\-\-pfilter\fR [val]
-: Filter out association test results with higher p\-values.
-.HP
-\fB\-\-aperm\fR [min perms \- 1] {max perms} {alpha} {beta} {init interval} {slope} :
-.IP
-Set up to six parameters controlling adaptive permutation tests.
-* The first two control the minimum and maximum number of permutations that
-.IP
-may be run for each variant; default values are 5 and 1000000.
-.TP
-* The next two control the early termination condition.
-A
-.IP
-100% * (1 \- beta/2T) confidence interval is calculated for each empirical
-p\-value, where T is the total number of variants; whenever this
-confidence interval doesn't contain alpha, the variant is exempted from
-further permutation testing. Default values are 0 and 1e\-4.
-.TP
-* The last two control when the early termination condition is checked.
-If
-.IP
-a check occurs at permutation #p, the next check occurs after
-[slope]p + [init interval] more permutations (rounded down). Default
-initial interval is 1, and default slope is 0.001.
-.TP
-\fB\-\-mperm\-save\fR
-: Save best max(T) permutation test statistics.
-.HP
-\fB\-\-mperm\-save\-all\fR : Save all max(T) permutation test statistics.
-.TP
-\fB\-\-set\-p\fR [p\-val]
-: Adjust set test significant variant p\-value ceiling
-(default 0.05).
-.TP
-\fB\-\-set\-r2\fR {v} <write>
-: Adjust set test significant variant pairwise r^2
-ceiling (default 0.5). 'write' causes violating
-pairs to be dumped to {output prefix}.ldset.
-.TP
-\fB\-\-set\-max\fR [ct]
-: Adjust set test maximum # of significant variants
-considered per set (default 5).
-.HP
-\fB\-\-set\-test\-lambda\fR [v] : Specify genomic control correction for set test.
-.TP
-\fB\-\-border\fR [kbs]
-: Extend \fB\-\-annotate\fR range intervals by given # kbs.
-.HP
-\fB\-\-annotate\-snp\-field\fR [nm] : Set \fB\-\-annotate\fR variant ID field name.
-.HP
-\fB\-\-clump\-p1\fR [pval] : Set \fB\-\-clump\fR index var. p\-value ceiling (default 1e\-4).
-.HP
-\fB\-\-clump\-p2\fR [pval] : Set \fB\-\-clump\fR secondary p\-value threshold (default 0.01).
-.TP
-\fB\-\-clump\-r2\fR [r^2]
-: Set \fB\-\-clump\fR r^2 threshold (default 0.5).
-.TP
-\fB\-\-clump\-kb\fR [kbs]
-: Set \fB\-\-clump\fR kb radius (default 250).
-.TP
-\fB\-\-clump\-snp\-field\fR [n...]
-: Set \fB\-\-clump\fR variant ID field name (default
-\&'SNP'). With multiple field names, earlier names
-take precedence over later ones.
-.TP
-\fB\-\-clump\-field\fR [name...]
-: Set \fB\-\-clump\fR p\-value field name (default 'P').
-.TP
-\fB\-\-clump\-allow\-overlap\fR
-: Let \fB\-\-clump\fR non\-index vars. join multiple clumps.
-.TP
-\fB\-\-clump\-verbose\fR
-: Request extended \fB\-\-clump\fR report.
-.TP
-\fB\-\-clump\-annotate\fR [hdr...] : Include named extra fields in \fB\-\-clump\-verbose\fR and
-\fB\-\-clump\-best\fR reports. (Field names can be
-separated with spaces or commas.)
-.TP
-\fB\-\-clump\-range\fR [filename]
-: Report overlaps between clumps and regions.
-.HP
-\fB\-\-clump\-range\-border\fR [kb] : Stretch regions in \fB\-\-clump\-range\fR file.
-.TP
-\fB\-\-clump\-index\-first\fR
-: Extract \fB\-\-clump\fR index vars. from only first file.
-.TP
-\fB\-\-clump\-replicate\fR
-: Exclude clumps which contain secondary results
-from only one file.
-.TP
-\fB\-\-clump\-best\fR
-: Report best proxy for each \fB\-\-clump\fR index var.
-.TP
-\fB\-\-gene\-list\-border\fR [kbs]
-: Extend \fB\-\-gene\-report\fR regions by given # of kbs.
-.TP
-\fB\-\-gene\-subset\fR [filename]
-: Specify gene name subset for \fB\-\-gene\-report\fR.
-.TP
-\fB\-\-gene\-report\-snp\-field\fR [] : Set \fB\-\-gene\-report\fR variant ID field name (default
-\&'SNP'). Only relevant with \fB\-\-extract\fR.
-.TP
-\fB\-\-gap\fR [kbs]
-: Set '\-\-fast\-epistasis case\-only' min. gap (default 1000).
-.TP
-\fB\-\-epi1\fR [p\-value] : Set \fB\-\-\fR{fast\-}epistasis reporting threshold (default
-5e\-6 for 'boost', 1e\-4 otherwise).
-.HP
-\fB\-\-epi2\fR [p\-value] : Set threshold for contributing to SIG_E count (def. 0.01).
-.TP
-\fB\-\-je\-cellmin\fR [n] : Set required number of observations per 3x3x2 contingency
-table cell for joint\-effects test (default 5).
-.HP
-\fB\-\-q\-score\-range\fR [range file] [data file] {i} {j} <header> :
-.IP
-Apply \fB\-\-score\fR to subset(s) of variants in the primary score list based
-on e.g. p\-value ranges.
-* The first file should have range labels in the first column, p\-value
-.IP
-lower bounds in the second column, and upper bounds in the third column.
-Lines with too few entries, or nonnumeric values in the second or third
-column, are ignored.
-.IP
-* The second file should contain a variant ID and a p\-value on each
-.TP
-nonempty line (except possibly the first).
-Variant IDs are read from
-.IP
-column #i and p\-values are read from column #j, where i defaults to 1 and
-j defaults to i+1. The 'header' modifier causes the first nonempty line
-of this file to be skipped.
-.TP
-\fB\-\-parallel\fR [k] [n] : Divide the output matrix into n pieces, and only compute
-the kth piece. The primary output file will have the
-piece number included in its name, e.g. plink.rel.13 or
-plink.rel.13.gz if k is 13. Concatenating these files
-in order will yield the full matrix of interest. (Yes,
-this can be done before unzipping.)
-N.B. This generally cannot be used to directly write a
-symmetric square matrix. Choose square0 or triangle
-shape instead, and postprocess as necessary.
-.TP
-\fB\-\-memory\fR [val]
-: Set size, in MB, of initial workspace malloc attempt.
-(Practically mandatory when using GNU parallel.)
-.TP
-\fB\-\-threads\fR [val]
-: Set maximum number of concurrent threads.
-.TP
-\fB\-\-d\fR [char]
-: Change variant/covariate range delimiter (normally '\-').
-.TP
-\fB\-\-seed\fR [val...]
-: Set random number seed(s). Each value must be an
-integer between 0 and 4294967295 inclusive.
-.TP
-\fB\-\-perm\-batch\-size\fR [val] : Set number of permutations per batch for some
-permutation tests.
-.TP
-\fB\-\-debug\fR
-: Use slower, more crash\-resistant logging method.
-.PP
-For further documentation and support, consult the main webpage
-(https://www.cog\-genomics.org/plink2 ) and/or the mailing list
-(https://groups.google.com/d/forum/plink2\-users ).
-.SH "SEE ALSO"
-The full documentation for
-.B PLINK
-is maintained as a Texinfo manual. If the
-.B info
-and
-.B PLINK
-programs are properly installed at your site, the command
-.IP
-.B info PLINK
-.PP
-should give you access to the complete manual.
diff --git a/debian/rules b/debian/rules
index d029f26..b05d628 100755
--- a/debian/rules
+++ b/debian/rules
@@ -13,5 +13,9 @@ override_dh_auto_clean:
dh_auto_clean
rm -f plink1.9
+override_dh_install:
+ help2man --no-discard-stderr --name="whole genome SNP analysis" ./plink1.9 > plink1.9.1
+ dh_install
+
get-orig-source:
uscan --verbose --force-download --repack --compress xz
diff --git a/debian/tests/output_tests/README.out b/debian/tests/output_tests/README
similarity index 61%
rename from debian/tests/output_tests/README.out
rename to debian/tests/output_tests/README
index 657830b..beed38c 100644
--- a/debian/tests/output_tests/README.out
+++ b/debian/tests/output_tests/README
@@ -1,10 +1,10 @@
-# Output files (i.e. plink.assoc and plink.frq) were generated following:
+# Output files (i.e. expected.plink.assoc and expected.plink.frq) were generated following:
wget https://www.cog-genomics.org/static/bin/plink141220/plink_linux_x86_64.zip
unzip plink_linux_x86_64.zip
./plink --file toy --freq
-mv plink.freq expected.plink.freq
+mv plink.frq expected.plink.frq
./plink --file toy --assoc
mv plink.assoc expected.plink.assoc
diff --git a/debian/tests/run-sample-analysis b/debian/tests/run-sample-analysis
index 51435ea..71ba2d1 100644
--- a/debian/tests/run-sample-analysis
+++ b/debian/tests/run-sample-analysis
@@ -11,14 +11,14 @@ fi
cd $ADTTMP
cp -a /usr/share/doc/${pkg}/examples/* $ADTTMP
-PLINK2_TEST='plink1.9 --file toy'
+PLINK19_TEST='plink1.9 --file toy'
# Allele frequencies
-$PLINK2_TEST --freq
+$PLINK19_TEST --freq
diff plink.frq expected.plink.frq
# Case/control or QTL association
-$PLINK2_TEST --assoc
+$PLINK19_TEST --assoc
diff plink.assoc expected.plink.assoc
rm -f $ADTTMP/*
--
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