[med-svn] [freebayes] 05/05: This are the autogenerated manpages. Just call debian/createmanpages after installing a higher version and watch the diff
Andreas Tille
tille at debian.org
Sat Jan 14 06:51:05 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch manpages
in repository freebayes.
commit bda11c8b5a0fc4f1fb346e8f16d9743bb3b980cf
Author: Andreas Tille <tille at debian.org>
Date: Sat Jan 14 07:50:05 2017 +0100
This are the autogenerated manpages. Just call debian/createmanpages after installing a higher version and watch the diff
---
debian/bamleftalign.1 | 8 ++--
debian/freebayes.1 | 101 +++++++++++++++++++++++++++++---------------------
2 files changed, 63 insertions(+), 46 deletions(-)
diff --git a/debian/bamleftalign.1 b/debian/bamleftalign.1
index db395a7..cc1e001 100644
--- a/debian/bamleftalign.1
+++ b/debian/bamleftalign.1
@@ -1,13 +1,13 @@
.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4.
.TH BAMLEFTALIGN "1" "January 2017" "bamleftalign 1.0.2" "User Commands"
.SH NAME
-bamleftalign \- Left\-aligns and merges the insertions and deletions in all alignments
-.SH SYNOPSIS
-[BAM data stream] | \fBbamleftalign\fR [options]
+bamleftalign \- <optional description of the program>
.SH DESCRIPTION
+usage: [BAM data stream] | bamleftalign [options]
+.PP
Left\-aligns and merges the insertions and deletions in all alignments in stdin.
Iterates until each alignment is stable through a left\-realignment step.
-.SH OPTIONS
+.SS "arguments:"
.TP
\fB\-f\fR \fB\-\-fasta\-reference\fR FILE
FASTA reference file to use for realignment (required)
diff --git a/debian/freebayes.1 b/debian/freebayes.1
index 70b8157..a697ebd 100644
--- a/debian/freebayes.1
+++ b/debian/freebayes.1
@@ -1,22 +1,23 @@
.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4.
.TH FREEBAYES "1" "January 2017" "freebayes 1.0.2" "User Commands"
.SH NAME
-freebayes \- Bayesian haplotype\-based polymorphism discovery
-.SH SYNOPSIS
-.B freebayes
-\fB\-f\fR [REFERENCE] [OPTIONS] [BAM FILES] >[OUTPUT]
+freebayes \- <optional description of the program>
.SH DESCRIPTION
-FreeBayes is a Bayesian genetic variant detector designed to find
-small polymorphisms, specifically SNPs (single-nucleotide
-polymorphisms), indels (insertions and deletions), MNPs
-(multi-nucleotide polymorphisms), and complex events (composite
-insertion and substitution events) smaller than the length of a
-short-read sequencing alignment.
-.SS Overview:
+usage: freebayes [OPTION] ... [BAM FILE] ...
+.PP
+Bayesian haplotype\-based polymorphism discovery.
+.PP
+citation: Erik Garrison, Gabor Marth
+.IP
+"Haplotype\-based variant detection from short\-read sequencing"
+arXiv:1207.3907 (http://arxiv.org/abs/1207.3907)
+.PP
+overview:
+.IP
To call variants from aligned short\-read sequencing data, supply BAM files and
a reference. FreeBayes will provide VCF output on standard out describing SNPs,
indels, and complex variants in samples in the input alignments.
-.PP
+.IP
By default, FreeBayes will consider variants supported by at least 2
observations in a single sample (\fB\-C\fR) and also by at least 20% of the reads from
a single sample (\fB\-F\fR). These settings are suitable to low to high depth
@@ -38,42 +39,49 @@ FreeBayes can act as a frequency\-based pooled caller and describe variants
and haplotypes in terms of observation frequency rather than called genotypes.
To do so, use \fB\-\-pooled\-continuous\fR and set input filters to a suitable level.
Allele observation counts will be described by AO and RO fields in the VCF output.
-.SH Examples
-.TP
+.PP
+examples:
+.IP
# call variants assuming a diploid sample
freebayes \fB\-f\fR ref.fa aln.bam >var.vcf
-.TP
+.IP
# call variants assuming a diploid sample, providing gVCF output
freebayes \fB\-f\fR ref.fa \fB\-\-gvcf\fR aln.bam >var.gvcf
-.TP
+.IP
# require at least 5 supporting observations to consider a variant
freebayes \fB\-f\fR ref.fa \fB\-C\fR 5 aln.bam >var.vcf
-.TP
+.IP
# use a different ploidy
freebayes \fB\-f\fR ref.fa \fB\-p\fR 4 aln.bam >var.vcf
-.TP
+.IP
# assume a pooled sample with a known number of genome copies
freebayes \fB\-f\fR ref.fa \fB\-p\fR 20 \fB\-\-pooled\-discrete\fR aln.bam >var.vcf
-.TP
+.IP
# generate frequency\-based calls for all variants passing input thresholds
freebayes \fB\-f\fR ref.fa \fB\-F\fR 0.01 \fB\-C\fR 1 \fB\-\-pooled\-continuous\fR aln.bam >var.vcf
-.TP
+.IP
# use an input VCF (bgzipped + tabix indexed) to force calls at particular alleles
freebayes \fB\-f\fR ref.fa \-@ in.vcf.gz aln.bam >var.vcf
-.TP
+.IP
# generate long haplotype calls over known variants
-freebayes \fB\-f\fR ref.fa \fB\-\-haplotype\-basis\-alleles\fR in.vcf.gz \fB\-\-haplotype\-length\fR 50 aln.bam
-.TP
+freebayes \fB\-f\fR ref.fa \fB\-\-haplotype\-basis\-alleles\fR in.vcf.gz \e
+.IP
+\fB\-\-haplotype\-length\fR 50 aln.bam
+.IP
# naive variant calling: simply annotate observation counts of SNPs and indels
-freebayes \fB\-f\fR ref.fa \fB\-\-haplotype\-length\fR 0 \fB\-\-min\-alternate\-count\fR 1 \fB\-\-min\-alternate\-fraction\fR 0 \fB\-\-pooled\-continuous\fR \fB\-\-report\-monomorphic\fR >var.vcf
-.SH OPTIONS
+freebayes \fB\-f\fR ref.fa \fB\-\-haplotype\-length\fR 0 \fB\-\-min\-alternate\-count\fR 1 \e
+.HP
+\fB\-\-min\-alternate\-fraction\fR 0 \fB\-\-pooled\-continuous\fR \fB\-\-report\-monomorphic\fR >var.vcf
+.PP
+parameters:
.TP
\fB\-h\fR \fB\-\-help\fR
Prints this help dialog.
.TP
\fB\-\-version\fR
Prints the release number and the git commit id.
-.SS input
+.PP
+input:
.TP
\fB\-b\fR \fB\-\-bam\fR FILE
Add FILE to the set of BAM files to be analyzed.
@@ -123,7 +131,8 @@ reference sequence, start, end, sample name, copy number
.IP
\&... for each region in each sample which does not have the
default copy number as set by \fB\-\-ploidy\fR.
-.SS output
+.PP
+output:
.TP
\fB\-v\fR \fB\-\-vcf\fR FILE
Output VCF\-format results to FILE. (default: stdout)
@@ -170,7 +179,8 @@ Loci which do not have any potential alternates have '.' for ALT.
\fB\-P\fR \fB\-\-pvar\fR N
Report sites if the probability that there is a polymorphism
at the site is greater than N. default: 0.0. Note that postfiltering is generally recommended over the use of this parameter.
-.SS population model
+.PP
+population model:
.TP
\fB\-T\fR \fB\-\-theta\fR N
The expected mutation rate or pairwise nucleotide diversity
@@ -193,7 +203,8 @@ per\-sample ploidy.
.IP
Output all alleles which pass input filters, regardles of
genotyping outcome or model.
-.SS reference allele
+.PP
+reference allele:
.HP
\fB\-Z\fR \fB\-\-use\-reference\-allele\fR
.IP
@@ -204,7 +215,8 @@ if it is another sample from the same population.
.IP
Assign mapping quality of MQ to the reference allele at each
site and base quality of BQ. default: 100,60
-.SS allele scope
+.PP
+allele scope:
.TP
\fB\-I\fR \fB\-\-no\-snps\fR
Ignore SNP alleles.
@@ -244,12 +256,14 @@ entropy > N bits per bp. (default: 0, off)
Exclude observations which do not fully span the dynamically\-determined
detection window. (default, use all observations, dividing partial
support across matching haplotypes when generating haplotypes.)
-.SS indel realignment
+.PP
+indel realignment:
.HP
\fB\-O\fR \fB\-\-dont\-left\-align\-indels\fR
.IP
Turn off left\-alignment of indels, which is enabled by default.
-.SS input filters
+.PP
+input filters:
.HP
\fB\-4\fR \fB\-\-use\-duplicate\-reads\fR
.IP
@@ -340,13 +354,15 @@ Require at least this coverage to process a site. default: 0
\fB\-\-max\-coverage\fR N
.IP
Do not process sites with greater than this coverage. default: no limit
-.SS population priors
+.PP
+population priors:
.HP
\fB\-k\fR \fB\-\-no\-population\-priors\fR
.IP
Equivalent to \fB\-\-pooled\-discrete\fR \fB\-\-hwe\-priors\-off\fR and removal of
Ewens Sampling Formula component of priors.
-.SS mappability priors
+.PP
+mappability priors:
.HP
\fB\-w\fR \fB\-\-hwe\-priors\-off\fR
.IP
@@ -364,7 +380,8 @@ and read position (5'\-3') probability.
.IP
Disable use of aggregate probability of observation balance between alleles
as a component of the priors.
-.SS genotype likelihoods
+.PP
+genotype likelihoods:
.HP
\fB\-\-observation\-bias\fR FILE
.IP
@@ -392,7 +409,8 @@ those generated by VerifyBamID. The format should be:
sample p(read=R|genotype=AR) p(read=A|genotype=AA)
.IP
Sample '*' can be used to set default contamination estimates.
-.SS algorithmic features
+.PP
+algorithmic features:
.HP
\fB\-\-report\-genotype\-likelihood\-max\fR
.IP
@@ -443,17 +461,16 @@ calculations. default: 0.9
.IP
Calculate the marginal probability of genotypes and report as GQ in
each sample field in the VCF output.
-.SS debugging
+.PP
+debugging:
.TP
\fB\-d\fR \fB\-\-debug\fR
Print debugging output.
.TP
\fB\-dd\fR
Print more verbose debugging output (requires "make DEBUG")
-.SH SEE ALSO
-"Haplotype\-based variant detection from short\-read sequencing"
-arXiv:1207.3907 (http://arxiv.org/abs/1207.3907)
+.PP
+author: Erik Garrison <erik.garrison at bc.edu>, Marth Lab, Boston College, 2010\-2014
+version: v1.0.0
.SH AUTHOR
-Erik Garrison <erik.garrison at bc.edu>, Marth Lab, Boston College, 2010\-2014, Gabor Marth
-.pp
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
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