[med-svn] r20509 - in trunk/packages/vcftools/trunk/debian: . mans
Andreas Tille
tille at moszumanska.debian.org
Mon Nov 16 14:36:55 UTC 2015
Author: tille
Date: 2015-11-16 14:36:54 +0000 (Mon, 16 Nov 2015)
New Revision: 20509
Added:
trunk/packages/vcftools/trunk/debian/mans/
trunk/packages/vcftools/trunk/debian/mans/fill-aa.1
trunk/packages/vcftools/trunk/debian/mans/fill-an-ac.1
trunk/packages/vcftools/trunk/debian/mans/fill-fs.1
trunk/packages/vcftools/trunk/debian/mans/fill-ref-md5.1
trunk/packages/vcftools/trunk/debian/mans/fill-rsIDs.1
trunk/packages/vcftools/trunk/debian/mans/vcf-annotate.1
trunk/packages/vcftools/trunk/debian/mans/vcf-compare.1
trunk/packages/vcftools/trunk/debian/mans/vcf-concat.1
trunk/packages/vcftools/trunk/debian/mans/vcf-consensus.1
trunk/packages/vcftools/trunk/debian/mans/vcf-contrast.1
trunk/packages/vcftools/trunk/debian/mans/vcf-convert.1
trunk/packages/vcftools/trunk/debian/mans/vcf-fix-ploidy.1
trunk/packages/vcftools/trunk/debian/mans/vcf-indel-stats.1
trunk/packages/vcftools/trunk/debian/mans/vcf-isec.1
trunk/packages/vcftools/trunk/debian/mans/vcf-merge.1
trunk/packages/vcftools/trunk/debian/mans/vcf-phased-join.1
trunk/packages/vcftools/trunk/debian/mans/vcf-query.1
trunk/packages/vcftools/trunk/debian/mans/vcf-shuffle-cols.1
trunk/packages/vcftools/trunk/debian/mans/vcf-sort.1
trunk/packages/vcftools/trunk/debian/mans/vcf-stats.1
trunk/packages/vcftools/trunk/debian/mans/vcf-subset.1
trunk/packages/vcftools/trunk/debian/mans/vcf-to-tab.1
trunk/packages/vcftools/trunk/debian/mans/vcf-tstv.1
trunk/packages/vcftools/trunk/debian/mans/vcf-validator.1
trunk/packages/vcftools/trunk/debian/mans/vcftools.1
Removed:
trunk/packages/vcftools/trunk/debian/README.source
trunk/packages/vcftools/trunk/debian/fill-aa.1
trunk/packages/vcftools/trunk/debian/fill-an-ac.1
trunk/packages/vcftools/trunk/debian/fill-fs.1
trunk/packages/vcftools/trunk/debian/fill-ref-md5.1
trunk/packages/vcftools/trunk/debian/fill-rsIDs.1
trunk/packages/vcftools/trunk/debian/vcf-annotate.1
trunk/packages/vcftools/trunk/debian/vcf-compare.1
trunk/packages/vcftools/trunk/debian/vcf-concat.1
trunk/packages/vcftools/trunk/debian/vcf-consensus.1
trunk/packages/vcftools/trunk/debian/vcf-contrast.1
trunk/packages/vcftools/trunk/debian/vcf-convert.1
trunk/packages/vcftools/trunk/debian/vcf-fix-ploidy.1
trunk/packages/vcftools/trunk/debian/vcf-indel-stats.1
trunk/packages/vcftools/trunk/debian/vcf-isec.1
trunk/packages/vcftools/trunk/debian/vcf-merge.1
trunk/packages/vcftools/trunk/debian/vcf-phased-join.1
trunk/packages/vcftools/trunk/debian/vcf-query.1
trunk/packages/vcftools/trunk/debian/vcf-shuffle-cols.1
trunk/packages/vcftools/trunk/debian/vcf-sort.1
trunk/packages/vcftools/trunk/debian/vcf-stats.1
trunk/packages/vcftools/trunk/debian/vcf-subset.1
trunk/packages/vcftools/trunk/debian/vcf-to-tab.1
trunk/packages/vcftools/trunk/debian/vcf-tstv.1
trunk/packages/vcftools/trunk/debian/vcf-validator.1
trunk/packages/vcftools/trunk/debian/vcftools.1
Modified:
trunk/packages/vcftools/trunk/debian/changelog
trunk/packages/vcftools/trunk/debian/makeman
trunk/packages/vcftools/trunk/debian/manpages
Log:
Remove redundant README.source; move manpages into common dir
Deleted: trunk/packages/vcftools/trunk/debian/README.source
===================================================================
--- trunk/packages/vcftools/trunk/debian/README.source 2015-11-16 14:23:28 UTC (rev 20508)
+++ trunk/packages/vcftools/trunk/debian/README.source 2015-11-16 14:36:54 UTC (rev 20509)
@@ -1,20 +0,0 @@
-vcftools - changes to source tree
-=================================
-
-A series of files and directories needed to be removed - nothing dramatic:
-
-$ find . -name ".svn"
-./website/img/.svn
-./website/src/.svn
-./website/.svn
-./cpp/.svn
-./examples/.svn
-./perl/.svn
-$ find . -name ".svn" | xargs -r rm -r
-$ find . -name "*.pdf"
-./website/VCF-poster.pdf
-$ find . -name "*.pdf" | xargs -r rm
-
-Also, the source tree has now the version number attached with a hyphen
-instead of an underscore.
-
Modified: trunk/packages/vcftools/trunk/debian/changelog
===================================================================
--- trunk/packages/vcftools/trunk/debian/changelog 2015-11-16 14:23:28 UTC (rev 20508)
+++ trunk/packages/vcftools/trunk/debian/changelog 2015-11-16 14:36:54 UTC (rev 20509)
@@ -1,4 +1,4 @@
-vcftools (0.1.14+dfsg-1) UNRELEASED; urgency=medium
+vcftools (0.1.14+dfsg-1) unstable; urgency=medium
* New upstream version
* Source has moved to github
@@ -6,8 +6,10 @@
* Remove unneeded get-orig-source script
* Adapt to new build system
* Delete unneeded overrides
+ * Remove redundant README.source
+ * move manpages into common dir
- -- Andreas Tille <tille at debian.org> Mon, 16 Nov 2015 14:09:02 +0100
+ -- Andreas Tille <tille at debian.org> Mon, 16 Nov 2015 15:25:49 +0100
vcftools (0.1.13+dfsg-1) unstable; urgency=medium
Deleted: trunk/packages/vcftools/trunk/debian/fill-aa.1
===================================================================
--- trunk/packages/vcftools/trunk/debian/fill-aa.1 2015-11-16 14:23:28 UTC (rev 20508)
+++ trunk/packages/vcftools/trunk/debian/fill-aa.1 2015-11-16 14:36:54 UTC (rev 20509)
@@ -1,13 +0,0 @@
-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.40.4.
-.TH FILL-AA "1" "July 2011" "fill-aa 0.1.5" "User Commands"
-.SH NAME
-fill-aa \- fill in ancestral alleles
-.SH SYNOPSIS
-.B fill-aa [OPTIONS]
-.SH DESCRIPTION
-.IP
-zcat file.vcf.gz | fill-aa \-a ancestral-alleles.fa.gz | bgzip \-c > out.vcf.gz
-.SH OPTIONS
-.TP
-\fB\-a\fR <file.gz>
-file containing acestral alleles
Deleted: trunk/packages/vcftools/trunk/debian/fill-an-ac.1
===================================================================
--- trunk/packages/vcftools/trunk/debian/fill-an-ac.1 2015-11-16 14:23:28 UTC (rev 20508)
+++ trunk/packages/vcftools/trunk/debian/fill-an-ac.1 2015-11-16 14:36:54 UTC (rev 20509)
@@ -1,9 +0,0 @@
-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.40.4.
-.TH FILL-AN-AC "1" "July 2011" "fill-an-ac 0.1.5" "User Commands"
-.SH NAME
-fill-an-ac \- fill or recalculate AN and AC INFO fields.
-.SH SYNOPSIS
-.B fill-an-ac
-.SH DESCRIPTION
-.IP
-zcat file.vcf.gz | fill-an-ac | bgzip \-c > out.vcf.gz
Deleted: trunk/packages/vcftools/trunk/debian/fill-fs.1
===================================================================
--- trunk/packages/vcftools/trunk/debian/fill-fs.1 2015-11-16 14:23:28 UTC (rev 20508)
+++ trunk/packages/vcftools/trunk/debian/fill-fs.1 2015-11-16 14:36:54 UTC (rev 20509)
@@ -1,39 +0,0 @@
-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.41.1.
-.TH FILL-FS "1" "February 2013" "fill-fs" "User Commands"
-.SH NAME
-fill-fs \- Annotate VCF with flanking sequence
-.SH SYNOPSIS
-.B fill-fs
-[\fIOPTIONS\fR] \fIfile.vcf\fR
-.SH DESCRIPTION
-About: Annotate VCF with flanking sequence (INFO/FS tag)
-.SH OPTIONS
-.TP
-\fB\-b\fR, \fB\-\-bed\-mask\fR <file>
-Regions to mask (tabix indexed), multiple files can be given
-.TP
-\fB\-c\fR, \fB\-\-cluster\fR <int>
-Do self\-masking of clustered variants within this range.
-.TP
-\fB\-l\fR, \fB\-\-length\fR <int>
-Flanking sequence length [100]
-.TP
-\fB\-m\fR, \fB\-\-mask\-char\fR <char|lc>
-The character to use or "lc" for lowercase. This option must preceed
-\fB\-b\fR, \fB\-v\fR or \fB\-c\fR in order to take effect. With multiple files works
-.IP
-as a switch on the command line, see the example below [N]
-.TP
-\fB\-r\fR, \fB\-\-refseq\fR <file>
-The reference sequence.
-.TP
-\fB\-v\fR, \fB\-\-vcf\-mask\fR <file>
-Mask known variants in the flanking sequence, multiple files can be given (tabix indexed)
-.TP
-\fB\-h\fR, \-?, \fB\-\-help\fR
-This help message.
-.SS "Example:"
-.IP
-# Mask variants from the VCF file with N's and use lowercase for the bed file regions
-fill\-fs file.vcf \fB\-v\fR mask.vcf \fB\-m\fR lc \fB\-b\fR mask.bed
-.IP
Deleted: trunk/packages/vcftools/trunk/debian/fill-ref-md5.1
===================================================================
--- trunk/packages/vcftools/trunk/debian/fill-ref-md5.1 2015-11-16 14:23:28 UTC (rev 20508)
+++ trunk/packages/vcftools/trunk/debian/fill-ref-md5.1 2015-11-16 14:36:54 UTC (rev 20509)
@@ -1,31 +0,0 @@
-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.41.1.
-.TH FILL-REF-MD5 "1" "February 2013" "fill-ref-md5" "User Commands"
-.SH NAME
-fill-ref-md5 \- computes MD5 sum of the reference sequence
-.SH SYNOPSIS
-.B fill-ref-md5
-[\fIOPTIONS\fR] \fIin.vcf.gz out.vcf.gz\fR
-.SH DESCRIPTION
-About: The script computes MD5 sum of the reference sequence and inserts
-.IP
-\&'reference' and 'contig' tags into header as recommended by VCFv4.1.
-The VCF file must be compressed and tabix indexed, as it takes advantage
-of the lightning fast tabix reheader functionality.
-.SH OPTIONS
-.TP
-\fB\-d\fR, \fB\-\-dictionary\fR <file>
-Where to read/write computed MD5s. Opened in append mode, existing records are not touched.
-.TP
-\fB\-i\fR, \fB\-\-info\fR <AS:xx,SP:xx,TX:xx>
-Optional info on reference assembly (AS), species (SP), taxonomy (TX)
-.TP
-\fB\-r\fR, \fB\-\-refseq\fR <file>
-The reference sequence in fasta format indexed by samtools faidx
-.TP
-\fB\-h\fR, \-?, \fB\-\-help\fR
-This help message.
-.SH EXAMPLES
-.TP
-fill\-ref\-md5 \-i AS:NCBIM37,SP:"Mus\e Musculus" \-r NCBIM37_um.fa
-\-d NCBIM37_um.fa.dict in.vcf.gz out.vcf.gz
-.IP
Deleted: trunk/packages/vcftools/trunk/debian/fill-rsIDs.1
===================================================================
--- trunk/packages/vcftools/trunk/debian/fill-rsIDs.1 2015-11-16 14:23:28 UTC (rev 20508)
+++ trunk/packages/vcftools/trunk/debian/fill-rsIDs.1 2015-11-16 14:36:54 UTC (rev 20509)
@@ -1,13 +0,0 @@
-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.40.4.
-.TH FILL-RSIDS "1" "July 2011" "fill-rsIDs 0.1.5" "User Commands"
-.SH NAME
-fill-rsIDs \- fill missing rsIDs
-.SH SYNOPSIS
-.B fill-rsIDs [OPTIONS]
-.SH DESCRIPTION
-.IP
-zcat file.vcf.gz | fill-rsIDs \-r dbSNP_ids_129.txt.bgz | bgzip \-c > out.vcf.gz
-.SH OPTIONS
-.TP
-\fB\-r\fR <file.bgz>
-file containing ids
Modified: trunk/packages/vcftools/trunk/debian/makeman
===================================================================
--- trunk/packages/vcftools/trunk/debian/makeman 2015-11-16 14:23:28 UTC (rev 20508)
+++ trunk/packages/vcftools/trunk/debian/makeman 2015-11-16 14:36:54 UTC (rev 20509)
@@ -1,16 +1,18 @@
#!/bin/bash
# helper script to create first version of man pages
-help2man -n "annotate VCF file, add filters or custom annotations" -N --help-option="-h" --no-discard-stderr --version-string="0.1.5" vcf-annotate > vcf-annotate.1
-help2man -n "compare bgzipped and tabix indexed VCF files" -N --help-option="-h" --no-discard-stderr --version-string="0.1.5" vcf-compare > vcf-compare.1
-help2man -n "concatenate VCF files" -N --help-option="-h" --no-discard-stderr --version-string="0.1.5" vcf-concat > vcf-concat.1
-help2man -n "convert between VCF versions" -N --help-option="-h" --no-discard-stderr --version-string="0.1.5" vcf-convert > vcf-convert.1
-help2man -n "create intersections, unions, complements on bgzipped and tabix indexed VCF or tab-delimited files" -N --help-option="-h" --no-discard-stderr --version-string="0.1.5" vcf-isec > vcf-isec.1
-help2man -n "merge the bgzipped and tabix indexed VCF files" -N --help-option="-h" --no-discard-stderr --version-string="0.1.5" vcf-merge > vcf-merge.1
-help2man -n "query VCF files" -N --help-option="-h" --no-discard-stderr --version-string="0.1.5" vcf-query > vcf-query.1
-help2man -n "sort VCF file" -N --help-option="-h" --no-discard-stderr --version-string="0.1.5" vcf-sort > vcf-sort.1
-help2man -n "statistic of VCF file" -N --help-option="-h" --no-discard-stderr --version-string="0.1.5" vcf-stats > vcf-stats.1
-help2man -n "create subset of VCF file" -N --help-option="-h" --no-discard-stderr --version-string="0.1.5" vcf-subset > vcf-subset.1
-help2man -n "convert to tabix" -N --help-option="-h" --no-discard-stderr --version-string="0.1.5" vcf-to-tab > vcf-to-tab.1
-help2man -n "validate VCF file" -N --help-option="-h" --no-discard-stderr --version-string="0.1.5" vcf-validator > vcf-validator.1
+MANDIR=mans
+help2man -n "annotate VCF file, add filters or custom annotations" -N --help-option="-h" --no-discard-stderr --version-string="0.1.5" vcf-annotate > ${MANDIR}/vcf-annotate.1
+help2man -n "compare bgzipped and tabix indexed VCF files" -N --help-option="-h" --no-discard-stderr --version-string="0.1.5" vcf-compare > ${MANDIR}/vcf-compare.1
+help2man -n "concatenate VCF files" -N --help-option="-h" --no-discard-stderr --version-string="0.1.5" vcf-concat > ${MANDIR}/vcf-concat.1
+help2man -n "convert between VCF versions" -N --help-option="-h" --no-discard-stderr --version-string="0.1.5" vcf-convert > ${MANDIR}/vcf-convert.1
+help2man -n "create intersections, unions, complements on bgzipped and tabix indexed VCF or tab-delimited files" -N --help-option="-h" --no-discard-stderr --version-string="0.1.5" vcf-isec > ${MANDIR}/vcf-isec.1
+help2man -n "merge the bgzipped and tabix indexed VCF files" -N --help-option="-h" --no-discard-stderr --version-string="0.1.5" vcf-merge > ${MANDIR}/vcf-merge.1
+help2man -n "query VCF files" -N --help-option="-h" --no-discard-stderr --version-string="0.1.5" vcf-query > ${MANDIR}/vcf-query.1
+help2man -n "sort VCF file" -N --help-option="-h" --no-discard-stderr --version-string="0.1.5" vcf-sort > ${MANDIR}/vcf-sort.1
+help2man -n "statistic of VCF file" -N --help-option="-h" --no-discard-stderr --version-string="0.1.5" vcf-stats > ${MANDIR}/vcf-stats.1
+help2man -n "create subset of VCF file" -N --help-option="-h" --no-discard-stderr --version-string="0.1.5" vcf-subset > ${MANDIR}/vcf-subset.1
+help2man -n "convert to tabix" -N --help-option="-h" --no-discard-stderr --version-string="0.1.5" vcf-to-tab > ${MANDIR}/vcf-to-tab.1
+help2man -n "validate VCF file" -N --help-option="-h" --no-discard-stderr --version-string="0.1.5" vcf-validator > ${MANDIR}/vcf-validator.1
+
Modified: trunk/packages/vcftools/trunk/debian/manpages
===================================================================
--- trunk/packages/vcftools/trunk/debian/manpages 2015-11-16 14:23:28 UTC (rev 20508)
+++ trunk/packages/vcftools/trunk/debian/manpages 2015-11-16 14:36:54 UTC (rev 20509)
@@ -1,25 +1 @@
-debian/vcftools.1
-debian/vcf-annotate.1
-debian/vcf-compare.1
-debian/vcf-concat.1
-debian/vcf-convert.1
-debian/vcf-isec.1
-debian/vcf-merge.1
-debian/vcf-query.1
-debian/vcf-sort.1
-debian/vcf-stats.1
-debian/vcf-subset.1
-debian/vcf-to-tab.1
-debian/vcf-validator.1
-debian/fill-aa.1
-debian/fill-an-ac.1
-debian/fill-rsIDs.1
-debian/fill-fs.1
-debian/fill-ref-md5.1
-debian/vcf-consensus.1
-debian/vcf-contrast.1
-debian/vcf-fix-ploidy.1
-debian/vcf-indel-stats.1
-debian/vcf-phased-join.1
-debian/vcf-shuffle-cols.1
-debian/vcf-tstv.1
+debian/mans/*.1
Copied: trunk/packages/vcftools/trunk/debian/mans/fill-aa.1 (from rev 20508, trunk/packages/vcftools/trunk/debian/fill-aa.1)
===================================================================
--- trunk/packages/vcftools/trunk/debian/mans/fill-aa.1 (rev 0)
+++ trunk/packages/vcftools/trunk/debian/mans/fill-aa.1 2015-11-16 14:36:54 UTC (rev 20509)
@@ -0,0 +1,13 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.40.4.
+.TH FILL-AA "1" "July 2011" "fill-aa 0.1.5" "User Commands"
+.SH NAME
+fill-aa \- fill in ancestral alleles
+.SH SYNOPSIS
+.B fill-aa [OPTIONS]
+.SH DESCRIPTION
+.IP
+zcat file.vcf.gz | fill-aa \-a ancestral-alleles.fa.gz | bgzip \-c > out.vcf.gz
+.SH OPTIONS
+.TP
+\fB\-a\fR <file.gz>
+file containing acestral alleles
Copied: trunk/packages/vcftools/trunk/debian/mans/fill-an-ac.1 (from rev 20508, trunk/packages/vcftools/trunk/debian/fill-an-ac.1)
===================================================================
--- trunk/packages/vcftools/trunk/debian/mans/fill-an-ac.1 (rev 0)
+++ trunk/packages/vcftools/trunk/debian/mans/fill-an-ac.1 2015-11-16 14:36:54 UTC (rev 20509)
@@ -0,0 +1,9 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.40.4.
+.TH FILL-AN-AC "1" "July 2011" "fill-an-ac 0.1.5" "User Commands"
+.SH NAME
+fill-an-ac \- fill or recalculate AN and AC INFO fields.
+.SH SYNOPSIS
+.B fill-an-ac
+.SH DESCRIPTION
+.IP
+zcat file.vcf.gz | fill-an-ac | bgzip \-c > out.vcf.gz
Copied: trunk/packages/vcftools/trunk/debian/mans/fill-fs.1 (from rev 20508, trunk/packages/vcftools/trunk/debian/fill-fs.1)
===================================================================
--- trunk/packages/vcftools/trunk/debian/mans/fill-fs.1 (rev 0)
+++ trunk/packages/vcftools/trunk/debian/mans/fill-fs.1 2015-11-16 14:36:54 UTC (rev 20509)
@@ -0,0 +1,39 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.41.1.
+.TH FILL-FS "1" "February 2013" "fill-fs" "User Commands"
+.SH NAME
+fill-fs \- Annotate VCF with flanking sequence
+.SH SYNOPSIS
+.B fill-fs
+[\fIOPTIONS\fR] \fIfile.vcf\fR
+.SH DESCRIPTION
+About: Annotate VCF with flanking sequence (INFO/FS tag)
+.SH OPTIONS
+.TP
+\fB\-b\fR, \fB\-\-bed\-mask\fR <file>
+Regions to mask (tabix indexed), multiple files can be given
+.TP
+\fB\-c\fR, \fB\-\-cluster\fR <int>
+Do self\-masking of clustered variants within this range.
+.TP
+\fB\-l\fR, \fB\-\-length\fR <int>
+Flanking sequence length [100]
+.TP
+\fB\-m\fR, \fB\-\-mask\-char\fR <char|lc>
+The character to use or "lc" for lowercase. This option must preceed
+\fB\-b\fR, \fB\-v\fR or \fB\-c\fR in order to take effect. With multiple files works
+.IP
+as a switch on the command line, see the example below [N]
+.TP
+\fB\-r\fR, \fB\-\-refseq\fR <file>
+The reference sequence.
+.TP
+\fB\-v\fR, \fB\-\-vcf\-mask\fR <file>
+Mask known variants in the flanking sequence, multiple files can be given (tabix indexed)
+.TP
+\fB\-h\fR, \-?, \fB\-\-help\fR
+This help message.
+.SS "Example:"
+.IP
+# Mask variants from the VCF file with N's and use lowercase for the bed file regions
+fill\-fs file.vcf \fB\-v\fR mask.vcf \fB\-m\fR lc \fB\-b\fR mask.bed
+.IP
Copied: trunk/packages/vcftools/trunk/debian/mans/fill-ref-md5.1 (from rev 20508, trunk/packages/vcftools/trunk/debian/fill-ref-md5.1)
===================================================================
--- trunk/packages/vcftools/trunk/debian/mans/fill-ref-md5.1 (rev 0)
+++ trunk/packages/vcftools/trunk/debian/mans/fill-ref-md5.1 2015-11-16 14:36:54 UTC (rev 20509)
@@ -0,0 +1,31 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.41.1.
+.TH FILL-REF-MD5 "1" "February 2013" "fill-ref-md5" "User Commands"
+.SH NAME
+fill-ref-md5 \- computes MD5 sum of the reference sequence
+.SH SYNOPSIS
+.B fill-ref-md5
+[\fIOPTIONS\fR] \fIin.vcf.gz out.vcf.gz\fR
+.SH DESCRIPTION
+About: The script computes MD5 sum of the reference sequence and inserts
+.IP
+\&'reference' and 'contig' tags into header as recommended by VCFv4.1.
+The VCF file must be compressed and tabix indexed, as it takes advantage
+of the lightning fast tabix reheader functionality.
+.SH OPTIONS
+.TP
+\fB\-d\fR, \fB\-\-dictionary\fR <file>
+Where to read/write computed MD5s. Opened in append mode, existing records are not touched.
+.TP
+\fB\-i\fR, \fB\-\-info\fR <AS:xx,SP:xx,TX:xx>
+Optional info on reference assembly (AS), species (SP), taxonomy (TX)
+.TP
+\fB\-r\fR, \fB\-\-refseq\fR <file>
+The reference sequence in fasta format indexed by samtools faidx
+.TP
+\fB\-h\fR, \-?, \fB\-\-help\fR
+This help message.
+.SH EXAMPLES
+.TP
+fill\-ref\-md5 \-i AS:NCBIM37,SP:"Mus\e Musculus" \-r NCBIM37_um.fa
+\-d NCBIM37_um.fa.dict in.vcf.gz out.vcf.gz
+.IP
Copied: trunk/packages/vcftools/trunk/debian/mans/fill-rsIDs.1 (from rev 20508, trunk/packages/vcftools/trunk/debian/fill-rsIDs.1)
===================================================================
--- trunk/packages/vcftools/trunk/debian/mans/fill-rsIDs.1 (rev 0)
+++ trunk/packages/vcftools/trunk/debian/mans/fill-rsIDs.1 2015-11-16 14:36:54 UTC (rev 20509)
@@ -0,0 +1,13 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.40.4.
+.TH FILL-RSIDS "1" "July 2011" "fill-rsIDs 0.1.5" "User Commands"
+.SH NAME
+fill-rsIDs \- fill missing rsIDs
+.SH SYNOPSIS
+.B fill-rsIDs [OPTIONS]
+.SH DESCRIPTION
+.IP
+zcat file.vcf.gz | fill-rsIDs \-r dbSNP_ids_129.txt.bgz | bgzip \-c > out.vcf.gz
+.SH OPTIONS
+.TP
+\fB\-r\fR <file.bgz>
+file containing ids
Copied: trunk/packages/vcftools/trunk/debian/mans/vcf-annotate.1 (from rev 20508, trunk/packages/vcftools/trunk/debian/vcf-annotate.1)
===================================================================
--- trunk/packages/vcftools/trunk/debian/mans/vcf-annotate.1 (rev 0)
+++ trunk/packages/vcftools/trunk/debian/mans/vcf-annotate.1 2015-11-16 14:36:54 UTC (rev 20509)
@@ -0,0 +1,84 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.40.4.
+.TH VCF-ANNOTATE "1" "July 2011" "vcf-annotate 0.1.5" "User Commands"
+.SH NAME
+vcf-annotate \- annotate VCF file, add filters or custom annotations
+.SH SYNOPSIS
+.B cat
+\fIin.vcf | vcf-annotate \fR[\fIOPTIONS\fR] \fI> out.vcf\fR
+.SH DESCRIPTION
+About: Annotates VCF file, adding filters or custom annotations. Requires tabix indexed file with annotations.
+.IP
+Currently annotates only the INFO column, but it will be extended on demand.
+.SH OPTIONS
+.TP
+\fB\-a\fR, \fB\-\-annotations\fR <file.gz>
+The tabix indexed file with the annotations: CHR\etFROM[\etTO][\etVALUE]+.
+.TP
+\fB\-c\fR, \fB\-\-columns\fR <list>
+The list of columns in the annotation file, e.g. CHROM,FROM,TO,\-,INFO/STR,INFO/GN. The dash
+in this example indicates that the third column should be ignored. If TO is not
+present, it is assumed that TO equals to FROM.
+.TP
+\fB\-d\fR, \fB\-\-description\fR <file|string>
+Header annotation, e.g. key=INFO,ID=HM2,Number=0,Type=Flag,Description='HapMap2 membership'.
+The descriptions can be read from a file, one annotation per line.
+.TP
+\fB\-f\fR, \fB\-\-filter\fR <list>
+Apply filters, list is in the format flt1=value/flt2/flt3=value/etc.
+.TP
+\fB\-h\fR, \-?, \fB\-\-help\fR
+This help message.
+.SS "Filters:"
+.TP
++
+Apply all filters with default values (can be overridden, see the example below).
+.TP
+\fB\-X\fR
+Exclude the filter X
+.TP
+1, StrandBias
+FLOAT Min P\-value for strand bias (given PV4) [0.0001]
+.TP
+2, BaseQualBias
+FLOAT Min P\-value for baseQ bias [1e\-100]
+.TP
+3, MapQualBias
+FLOAT Min P\-value for mapQ bias [0]
+.TP
+4, EndDistBias
+FLOAT Min P\-value for end distance bias [0.0001]
+.TP
+a, MinAB
+INT Minimum number of alternate bases [2]
+.TP
+c, SnpCluster
+INT1,INT2 Filters clusters of 'INT1' or more SNPs within a run of 'INT2' bases []
+.TP
+D, MaxDP
+INT Maximum read depth [10000000]
+.TP
+d, MinDP
+INT Minimum read depth [2]
+.TP
+q, MinMQ
+INT Minimum RMS mapping quality for SNPs [10]
+.TP
+Q, Qual
+INT Minimum value of the QUAL field [10]
+.TP
+r, RefN
+Reference base is N []
+.TP
+W, GapWin
+INT Window size for filtering adjacent gaps [10]
+.TP
+w, SnpGap
+INT SNP within INT bp around a gap to be filtered [10]
+.SS "Example:"
+.IP
+zcat in.vcf.gz | vcf\-annotate \fB\-a\fR annotations.gz \fB\-d\fR descriptions.txt | bgzip \fB\-c\fR >out.vcf.gz
+zcat in.vcf.gz | vcf\-annotate \fB\-f\fR +/\-a/c=3,10/q=3/d=5/\-D \fB\-a\fR annotations.gz \fB\-d\fR descriptions.txt | bgzip \fB\-c\fR >out.vcf.gz
+.SS "Where descriptions.txt contains:"
+.IP
+key=INFO,ID=GN,Number=1,Type=String,Description='Gene Name'
+key=INFO,ID=STR,Number=1,Type=Integer,Description='Strand'
Copied: trunk/packages/vcftools/trunk/debian/mans/vcf-compare.1 (from rev 20508, trunk/packages/vcftools/trunk/debian/vcf-compare.1)
===================================================================
--- trunk/packages/vcftools/trunk/debian/mans/vcf-compare.1 (rev 0)
+++ trunk/packages/vcftools/trunk/debian/mans/vcf-compare.1 2015-11-16 14:36:54 UTC (rev 20509)
@@ -0,0 +1,40 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.40.4.
+.TH VCF-COMPARE "1" "July 2011" "vcf-compare 0.1.5" "User Commands"
+.SH NAME
+vcf-compare \- compare bgzipped and tabix indexed VCF files
+.SH SYNOPSIS
+.B compare-vcf
+[\fIOPTIONS\fR] \fIfile1.vcf file2.vcf \fR...
+.SH DESCRIPTION
+About: Compare bgzipped and tabix indexed VCF files. (E.g. bgzip file.vcf; tabix \fB\-p\fR vcf file.vcf.gz)
+.SH OPTIONS
+.TP
+\fB\-c\fR, \fB\-\-chromosomes\fR <list|file>
+Same as \fB\-r\fR, left for backward compatibility. Please do not use as it will be dropped in the future.
+.TP
+\fB\-d\fR, \fB\-\-debug\fR
+Debugging information. Giving the option multiple times increases verbosity
+.TP
+\fB\-H\fR, \fB\-\-cmp\-haplotypes\fR
+Compare haplotypes, not only positions
+.TP
+\fB\-m\fR, \fB\-\-name\-mapping\fR <list|file>
+Use with \fB\-H\fR when comparing files with differing column names. The argument to this options is a
+comma\-separated list or one mapping per line in a file. The names are colon separated and must
+appear in the same order as the files on the command line.
+.TP
+\fB\-R\fR, \fB\-\-refseq\fR <file>
+Compare the actual sequence, not just positions. Use with \fB\-w\fR to compare indels.
+.TP
+\fB\-r\fR, \fB\-\-regions\fR <list|file>
+Process the given regions (comma\-separated list or one region per line in a file).
+.TP
+\fB\-s\fR, \fB\-\-samples\fR <list>
+Process only the listed samples. Excluding unwanted samples may increase performance considerably.
+.TP
+\fB\-w\fR, \fB\-\-win\fR <int>
+In repetitive sequences, the same indel can be called at different positions. Consider
+records this far apart as matching (be it a SNP or an indel).
+.TP
+\fB\-h\fR, \-?, \fB\-\-help\fR
+This help message.
Copied: trunk/packages/vcftools/trunk/debian/mans/vcf-concat.1 (from rev 20508, trunk/packages/vcftools/trunk/debian/vcf-concat.1)
===================================================================
--- trunk/packages/vcftools/trunk/debian/mans/vcf-concat.1 (rev 0)
+++ trunk/packages/vcftools/trunk/debian/mans/vcf-concat.1 2015-11-16 14:36:54 UTC (rev 20509)
@@ -0,0 +1,23 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.40.4.
+.TH VCF-CONCAT "1" "July 2011" "vcf-concat 0.1.5" "User Commands"
+.SH NAME
+vcf-concat \- concatenate VCF files
+.SH SYNOPSIS
+.B vcf-concat
+[\fIOPTIONS\fR] \fIA.vcf.gz B.vcf.gz C.vcf.gz > out.vcf\fR
+.SH DESCRIPTION
+About: Convenience tool for concatenating VCF files. In the basic mode it does not
+.IP
+do anything fancy except for a sanity check that all files have the same columns.
+When run with the \fB\-s\fR option, it will perform a partial merge sort, looking at
+a limited number of open jobs simultaneously.
+.SH OPTIONS
+.TP
+\fB\-f\fR, \fB\-\-files\fR <file>
+Read the list of files from a file.
+.TP
+\fB\-s\fR, \fB\-\-merge\-sort\fR <int>
+Allow small overlaps in N consecutive files.
+.TP
+\fB\-h\fR, \-?, \fB\-\-help\fR
+This help message.
Copied: trunk/packages/vcftools/trunk/debian/mans/vcf-consensus.1 (from rev 20508, trunk/packages/vcftools/trunk/debian/vcf-consensus.1)
===================================================================
--- trunk/packages/vcftools/trunk/debian/mans/vcf-consensus.1 (rev 0)
+++ trunk/packages/vcftools/trunk/debian/mans/vcf-consensus.1 2015-11-16 14:36:54 UTC (rev 20509)
@@ -0,0 +1,14 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.41.1.
+.TH VCF-CONSENSUS "1" "February 2013" "vcf-consensus" "User Commands"
+.SH NAME
+vcf-consensus \- vcf-consensus
+.SH SYNOPSIS
+.B cat
+\fIref.fa | vcf-consensus \fR[\fIOPTIONS\fR] \fIin.vcf.gz > out.txt\fR
+.SH OPTIONS
+.TP
+\fB\-h\fR, \-?, \fB\-\-help\fR
+This help message.
+.HP
+\fB\-s\fR, \fB\-\-sample\fR <name>
+.IP
Copied: trunk/packages/vcftools/trunk/debian/mans/vcf-contrast.1 (from rev 20508, trunk/packages/vcftools/trunk/debian/vcf-contrast.1)
===================================================================
--- trunk/packages/vcftools/trunk/debian/mans/vcf-contrast.1 (rev 0)
+++ trunk/packages/vcftools/trunk/debian/mans/vcf-contrast.1 2015-11-16 14:36:54 UTC (rev 20509)
@@ -0,0 +1,39 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.41.1.
+.TH VCF-CONTRAST "1" "February 2013" "vcf-contrast" "User Commands"
+.SH NAME
+vcf-contrast \- finds differences amongst samples
+.SH SYNOPSIS
+.B vcf-contrast
+\fI+<list> -<list> \fR[\fIOPTIONS\fR] \fIfile.vcf.gz\fR
+.SH DESCRIPTION
+About: Finds differences amongst samples adding NOVEL* annotation to INFO field.
+.SH OPTIONS
+.TP
++<list>
+List of samples where unique variant is expected
+.TP
+\-<list>
+List of background samples
+.TP
+\fB\-d\fR, \fB\-\-min\-DP\fR <int>
+Minimum depth across all \-<list> samples
+.TP
+\fB\-f\fR, \fB\-\-apply\-filters\fR
+Skip sites with FILTER column different from PASS or "."
+.TP
+\fB\-n\fR, \fB\-\-novel\-sites\fR
+Print only records with novel genotypes
+.TP
+\fB\-h\fR, \-?, \fB\-\-help\fR
+This help message.
+.SS "Example:"
+.IP
+# Test if any of the samples A,B is different from all C,D,E
+vcf\-contrast +A,B \fB\-C\fR,D,E \fB\-m\fR file.vcf.gz
+.IP
+# Same as above but printing only sites with novel variants and table output
+vcf\-contrast \fB\-n\fR +A,B \fB\-C\fR,D,E \fB\-m\fR file.vcf.gz | vcf\-query \fB\-f\fR '%CHROM %POS\et%INFO/NOVELTY\et%INFO/NOVELAL\et%INFO/NOVELGT[\et%SAMPLE %GTR %PL]\en'
+.IP
+# Similar to above but require minimum mapping quality of 20
+vcf\-annotate \fB\-f\fR MinMQ=20 file.vcf.gz | vcf\-contrast +A,B,C \fB\-D\fR,E,F \fB\-f\fR
+.IP
Copied: trunk/packages/vcftools/trunk/debian/mans/vcf-convert.1 (from rev 20508, trunk/packages/vcftools/trunk/debian/vcf-convert.1)
===================================================================
--- trunk/packages/vcftools/trunk/debian/mans/vcf-convert.1 (rev 0)
+++ trunk/packages/vcftools/trunk/debian/mans/vcf-convert.1 2015-11-16 14:36:54 UTC (rev 20509)
@@ -0,0 +1,19 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.40.4.
+.TH VCF-CONVERT "1" "July 2011" "vcf-convert 0.1.5" "User Commands"
+.SH NAME
+vcf-convert \- convert between VCF versions
+.SH SYNOPSIS
+.B cat
+\fIin.vcf | vcf-convert \fR[\fIOPTIONS\fR] \fI> out.vcf\fR
+.SH DESCRIPTION
+About: Convert between VCF versions, currently to VCFv4.0 only.
+.SH OPTIONS
+.TP
+\fB\-r\fR, \fB\-\-refseq\fR <file>
+The reference sequence in samtools faindexed fasta file. (Not required with SNPs only.)
+.TP
+\fB\-v\fR, \fB\-\-version\fR <string>
+4.0
+.TP
+\fB\-h\fR, \-?, \fB\-\-help\fR
+This help message.
Copied: trunk/packages/vcftools/trunk/debian/mans/vcf-fix-ploidy.1 (from rev 20508, trunk/packages/vcftools/trunk/debian/vcf-fix-ploidy.1)
===================================================================
--- trunk/packages/vcftools/trunk/debian/mans/vcf-fix-ploidy.1 (rev 0)
+++ trunk/packages/vcftools/trunk/debian/mans/vcf-fix-ploidy.1 2015-11-16 14:36:54 UTC (rev 20509)
@@ -0,0 +1,52 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.41.1.
+.TH VCF-FIX-PLOIDY "1" "February 2013" "vcf-fix-ploidy" "User Commands"
+.SH NAME
+vcf-fix-ploidy \- vcf-fix-ploidy
+.SH SYNOPSIS
+.B cat
+\fIbroken.vcf | vcf-fix-ploidy \fR[\fIOPTIONS\fR] \fI> fixed.vcf\fR
+.SH OPTIONS
+.TP
+\fB\-a\fR, \fB\-\-assumed\-sex\fR <sex>
+M or F, required if the list is not complete in \fB\-s\fR
+.TP
+\fB\-l\fR, \fB\-\-fix\-likelihoods\fR
+Add or remove het likelihoods (not the default behaviour)
+.TP
+\fB\-p\fR, \fB\-\-ploidy\fR <file>
+Ploidy definition. The default is shown below.
+.TP
+\fB\-s\fR, \fB\-\-samples\fR <file>
+List of sample sexes (sample_name [MF]).
+.TP
+\fB\-h\fR, \-?, \fB\-\-help\fR
+This help message.
+.SS "Default ploidy definition:"
+.IP
+ploidy =>
+{
+.IP
+X =>
+[
+.IP
+# The pseudoautosomal regions 60,001\-2,699,520 and 154,931,044\-155,270,560 with the ploidy 2
+{ from=>1, to=>60_000, M=>1 },
+{ from=>2_699_521, to=>154_931_043, M=>1 },
+.IP
+],
+Y =>
+[
+.IP
+# No chrY in females and one copy in males
+{ from=>1, to=>59_373_566, M=>1, F=>0 },
+.IP
+],
+MT =>
+[
+.IP
+# Haploid MT in males and females
+{ from=>1, to => 16_569, M=>1, F=>1 },
+.IP
+],
+.IP
+}
Copied: trunk/packages/vcftools/trunk/debian/mans/vcf-indel-stats.1 (from rev 20508, trunk/packages/vcftools/trunk/debian/vcf-indel-stats.1)
===================================================================
--- trunk/packages/vcftools/trunk/debian/mans/vcf-indel-stats.1 (rev 0)
+++ trunk/packages/vcftools/trunk/debian/mans/vcf-indel-stats.1 2015-11-16 14:36:54 UTC (rev 20509)
@@ -0,0 +1,19 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.41.1.
+.TH VCF-INDEL-STATS "1" "February 2013" "vcf-indel-stats" "User Commands"
+.SH NAME
+vcf-indel-stats \- vcf-indel-stat
+.SH SYNOPSIS
+.B vcf-indel-stats
+[\fIOPTIONS\fR] \fI< in.vcf > out.txt\fR
+.SH DESCRIPTION
+About: Currently calculates in\-frame ratio.
+.SH OPTIONS
+.TP
+\fB\-h\fR, \-?, \fB\-\-help\fR
+This help message.
+.TP
+\fB\-e\fR, \fB\-\-exons\fR <file>
+Tab\-separated file with exons (chr,from,to; 1\-based, inclusive)
+.HP
+\fB\-v\fR, \fB\-\-verbose\fR
+.IP
Copied: trunk/packages/vcftools/trunk/debian/mans/vcf-isec.1 (from rev 20508, trunk/packages/vcftools/trunk/debian/vcf-isec.1)
===================================================================
--- trunk/packages/vcftools/trunk/debian/mans/vcf-isec.1 (rev 0)
+++ trunk/packages/vcftools/trunk/debian/mans/vcf-isec.1 2015-11-16 14:36:54 UTC (rev 20509)
@@ -0,0 +1,48 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.40.4.
+.TH VCF-ISEC "1" "July 2011" "vcf-isec 0.1.5" "User Commands"
+.SH NAME
+vcf-isec \- create intersections, unions, complements on bgzipped and tabix indexed VCF or tab-delimited files
+.SH SYNOPSIS
+.B vcf-isec
+[\fIOPTIONS\fR] \fIfile1.vcf file2.vcf \fR...
+.SH DESCRIPTION
+About: Create intersections, unions, complements on bgzipped and tabix indexed VCF or tab\-delimited files.
+.IP
+Note that lines from all files can be intermixed together on the output, which can yield
+unexpected results.
+.SH OPTIONS
+.TP
+\fB\-C\fR, \fB\-\-chromosomes\fR <list|file>
+Process the given chromosomes (comma\-separated list or one chromosome per line in a file).
+.TP
+\fB\-c\fR, \fB\-\-complement\fR
+Output positions present in the first file but missing from the other files.
+.TP
+\fB\-d\fR, \fB\-\-debug\fR
+Debugging information
+.TP
+\fB\-f\fR, \fB\-\-force\fR
+Continue even if the script complains about differing columns.
+.TP
+\fB\-o\fR, \fB\-\-one\-file\-only\fR
+Print only entries from the left\-most file. Without \fB\-o\fR, all unique positions will be printed.
+.TP
+\fB\-n\fR, \fB\-\-nfiles\fR [+\-=]<int>
+Output positions present in this many (=), this many or more (+), or this many or fewer (\-) files.
+.TP
+\fB\-p\fR, \fB\-\-prefix\fR <path>
+If present, multiple files will be created with all possible isec combinations. (Suitable for Venn Diagram analysis.)
+.TP
+\fB\-t\fR, \fB\-\-tab\fR <chr:pos:file>
+Tab\-delimited file with indexes of chromosome and position columns. (1\-based indexes)
+.TP
+\fB\-w\fR, \fB\-\-win\fR <int>
+In repetitive sequences, the same indel can be called at different positions. Consider
+records this far apart as matching (be it a SNP or an indel).
+.TP
+\fB\-h\fR, \-?, \fB\-\-help\fR
+This help message.
+.SH EXAMPLES
+.IP
+bgzip file.vcf; tabix \fB\-p\fR vcf file.vcf.gz
+bgzip file.tab; tabix \fB\-s\fR 1 \fB\-b\fR 2 \fB\-e\fR 2 file.tab.gz
Copied: trunk/packages/vcftools/trunk/debian/mans/vcf-merge.1 (from rev 20508, trunk/packages/vcftools/trunk/debian/vcf-merge.1)
===================================================================
--- trunk/packages/vcftools/trunk/debian/mans/vcf-merge.1 (rev 0)
+++ trunk/packages/vcftools/trunk/debian/mans/vcf-merge.1 2015-11-16 14:36:54 UTC (rev 20509)
@@ -0,0 +1,28 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.40.4.
+.TH VCF-MERGE "1" "July 2011" "vcf-merge 0.1.5" "User Commands"
+.SH NAME
+vcf-merge \- merge the bgzipped and tabix indexed VCF files
+.SH SYNOPSIS
+.B merge-vcf
+[\fIOPTIONS\fR] \fIfile1.vcf file2.vcf.gz \fR... \fI> out.vcf\fR
+.SH DESCRIPTION
+About: Merge the bgzipped and tabix indexed VCF files. (E.g. bgzip file.vcf; tabix \fB\-p\fR vcf file.vcf.gz)
+.SH OPTIONS
+.TP
+\fB\-c\fR, \fB\-\-chromosomes\fR <list|file>
+Same as \fB\-r\fR, left for backward compatibility. Please do not use as it will be dropped in the future.
+.TP
+\fB\-d\fR, \fB\-\-remove\-duplicates\fR
+If there should be two consecutive rows with the same chr:pos, print only the first one.
+.TP
+\fB\-H\fR, \fB\-\-vcf\-header\fR <file>
+Use the VCF header
+.TP
+\fB\-h\fR, \-?, \fB\-\-help\fR
+This help message.
+.TP
+\fB\-r\fR, \fB\-\-regions\fR <list|file>
+Do only the given regions (comma\-separated list or one region per line in a file).
+.TP
+\fB\-s\fR, \fB\-\-silent\fR
+Try to be a bit more silent, no warnings about duplicate lines.
Copied: trunk/packages/vcftools/trunk/debian/mans/vcf-phased-join.1 (from rev 20508, trunk/packages/vcftools/trunk/debian/vcf-phased-join.1)
===================================================================
--- trunk/packages/vcftools/trunk/debian/mans/vcf-phased-join.1 (rev 0)
+++ trunk/packages/vcftools/trunk/debian/mans/vcf-phased-join.1 2015-11-16 14:36:54 UTC (rev 20509)
@@ -0,0 +1,28 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.41.1.
+.TH VCF-PHASED-JOIN "1" "February 2013" "vcf-phased-join" "User Commands"
+.SH NAME
+vcf-phased-join \- take multiple overlapping pre\-phased chunks and concatenates them into one VCF
+.SH SYNOPSIS
+.B vcf-phased-join
+[\fIOPTIONS\fR] \fIA.vcf B.vcf C.vcf\fR
+.SH DESCRIPTION
+About: The script takes multiple overlapping pre\-phased chunks and concatenates them into one VCF
+.IP
+using heterozygous calls from the overlaps to determine correct phase.
+.SH OPTIONS
+.TP
+\fB\-j\fR, \fB\-\-min\-join\-quality\fR <num>
+Quality threshold for gluing the pre\-phased blocks together [10]
+.TP
+\fB\-l\fR, \fB\-\-list\fR <file>
+List of VCFs to join.
+.TP
+\fB\-o\fR, \fB\-\-output\fR <file>
+Output file name. When "\-" is supplied, STDOUT and STDERR will be used
+.TP
+\fB\-q\fR, \fB\-\-min\-PQ\fR <num>
+Break pre\-phased segments if PQ value is lower in input VCFs [0.6]
+.TP
+\fB\-h\fR, \-?, \fB\-\-help\fR
+This help message
+.IP
Copied: trunk/packages/vcftools/trunk/debian/mans/vcf-query.1 (from rev 20508, trunk/packages/vcftools/trunk/debian/vcf-query.1)
===================================================================
--- trunk/packages/vcftools/trunk/debian/mans/vcf-query.1 (rev 0)
+++ trunk/packages/vcftools/trunk/debian/mans/vcf-query.1 2015-11-16 14:36:54 UTC (rev 20509)
@@ -0,0 +1,29 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.40.4.
+.TH VCF-QUERY "1" "July 2011" "vcf-query 0.1.5" "User Commands"
+.SH NAME
+vcf-query \- query VCF files
+.SH SYNOPSIS
+.B query-vcf
+[\fIOPTIONS\fR] \fIfile.vcf.gz\fR
+.SH OPTIONS
+.TP
+\fB\-c\fR, \fB\-\-columns\fR <NA001,NA002,..>
+List of comma\-separated column names.
+.TP
+\fB\-f\fR, \fB\-\-format\fR <string>
+The default is '%CHROM:%POS\et%REF[\et%SAMPLE=%GT]\en'
+.TP
+\fB\-l\fR, \fB\-\-list\-columns\fR
+List columns.
+.TP
+\fB\-r\fR, \fB\-\-region\fR chr:from\-to
+Retrieve the region. (Runs tabix.)
+.TP
+\fB\-h\fR, \-?, \fB\-\-help\fR
+This help message.
+.SH EXAMPLES
+.IP
+query\-vcf file.vcf.gz 1:1000\-2000 \fB\-c\fR NA001,NA002,NA003
+query\-vcf file.vcf.gz \fB\-r\fR 1:1000\-2000 \fB\-f\fR '%CHROM:%POS\et%REF[\et%SAMPLE:%*=,]\en'
+query\-vcf file.vcf.gz \fB\-f\fR '[%GT\et]%LINE\en'
+query\-vcf file.vcf.gz \fB\-f\fR '%CHROM\et%POS\et%INFO/DP\et%FILTER\en'
Copied: trunk/packages/vcftools/trunk/debian/mans/vcf-shuffle-cols.1 (from rev 20508, trunk/packages/vcftools/trunk/debian/vcf-shuffle-cols.1)
===================================================================
--- trunk/packages/vcftools/trunk/debian/mans/vcf-shuffle-cols.1 (rev 0)
+++ trunk/packages/vcftools/trunk/debian/mans/vcf-shuffle-cols.1 2015-11-16 14:36:54 UTC (rev 20509)
@@ -0,0 +1,17 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.41.1.
+.TH VCF-SHUFFLE-COLS "1" "February 2013" "vcf-shuffle-cols" "User Commands"
+.SH NAME
+vcf-shuffle-cols \- reorder columns
+.SH SYNOPSIS
+.B vcf-shuffle-cols
+[\fIOPTIONS\fR] \fI-t template.vcf.gz file.vcf.gz > out.vcf\fR
+.SH DESCRIPTION
+About: Reorder columns to match the order in the template VCF.
+.SH OPTIONS
+.TP
+\fB\-t\fR, \fB\-\-template\fR <file>
+The file with the correct order of the columns.
+.TP
+\fB\-h\fR, \-?, \fB\-\-help\fR
+This help message.
+.IP
Copied: trunk/packages/vcftools/trunk/debian/mans/vcf-sort.1 (from rev 20508, trunk/packages/vcftools/trunk/debian/vcf-sort.1)
===================================================================
--- trunk/packages/vcftools/trunk/debian/mans/vcf-sort.1 (rev 0)
+++ trunk/packages/vcftools/trunk/debian/mans/vcf-sort.1 2015-11-16 14:36:54 UTC (rev 20509)
@@ -0,0 +1,14 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.40.4.
+.TH VCF-SORT "1" "July 2011" "vcf-sort 0.1.5" "User Commands"
+.SH NAME
+vcf-sort \- sort VCF file
+.SH SYNOPSIS
+.B vcf-sort
+\fI> out.vcf\fR
+.SH DESCRIPTION
+.IP
+cat file.vcf | vcf\-sort > out.vcf
+.SH OPTIONS
+.TP
+\fB\-h\fR, \-?, \fB\-\-help\fR
+This help message.
Copied: trunk/packages/vcftools/trunk/debian/mans/vcf-stats.1 (from rev 20508, trunk/packages/vcftools/trunk/debian/vcf-stats.1)
===================================================================
--- trunk/packages/vcftools/trunk/debian/mans/vcf-stats.1 (rev 0)
+++ trunk/packages/vcftools/trunk/debian/mans/vcf-stats.1 2015-11-16 14:36:54 UTC (rev 20509)
@@ -0,0 +1,35 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.40.4.
+.TH VCF-STATS "1" "July 2011" "vcf-stats 0.1.5" "User Commands"
+.SH NAME
+vcf-stats \- statistic of VCF file
+.SH SYNOPSIS
+.B vcf-stats
+[\fIOPTIONS\fR] \fIfile.vcf.gz\fR
+.SH OPTIONS
+.TP
+\fB\-d\fR, \fB\-\-dump\fR <file>
+Take an existing dump file and recreate the files (works with \fB\-p\fR)
+.TP
+\fB\-f\fR, \fB\-\-filters\fR <filter1,filter2>
+List of filters such as column/field (any value), column/field=bin:max (cluster in bins),column/field=value (exact value)
+.TP
+\fB\-p\fR, \fB\-\-prefix\fR <dir/string>
+Prefix of output files. If slashes are present, directories will be created.
+.TP
+\fB\-s\fR, \fB\-\-samples\fR <list>
+Process only the listed samples, \- for none. Excluding unwanted samples may increase performance considerably.
+.TP
+\fB\-h\fR, \-?, \fB\-\-help\fR
+This help message.
+.SH EXAMPLES
+.IP
+# Calculate stats separately for the filter field, quality and non\-indels
+vcf\-stats file.vcf.gz \fB\-f\fR FILTER,QUAL=10:200,INFO/INDEL=False \fB\-p\fR out/
+.IP
+# Calculate stats for all samples
+vcf\-stats file.vcf.gz \fB\-f\fR FORMAT/DP=10:200 \fB\-p\fR out/
+.IP
+# Calculate stats only for the sample NA00001
+vcf\-stats file.vcf.gz \fB\-f\fR SAMPLE/NA00001/DP=1:200 \fB\-p\fR out/
+.IP
+vcf\-stats file.vcf.gz > perl.dump
Copied: trunk/packages/vcftools/trunk/debian/mans/vcf-subset.1 (from rev 20508, trunk/packages/vcftools/trunk/debian/vcf-subset.1)
===================================================================
--- trunk/packages/vcftools/trunk/debian/mans/vcf-subset.1 (rev 0)
+++ trunk/packages/vcftools/trunk/debian/mans/vcf-subset.1 2015-11-16 14:36:54 UTC (rev 20509)
@@ -0,0 +1,32 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.40.4.
+.TH VCF-SUBSET "1" "July 2011" "vcf-subset 0.1.5" "User Commands"
+.SH NAME
+vcf-subset \- create subset of VCF file
+.SH SYNOPSIS
+.B vcf-subset
+[\fIOPTIONS\fR] \fIin.vcf.gz > out.vcf\fR
+.SH OPTIONS
+.TP
+\fB\-c\fR, \fB\-\-columns\fR <string>
+File or comma\-separated list of columns to keep in the vcf file. If file, one column per row
+.TP
+\fB\-e\fR, \fB\-\-exclude\-ref\fR
+Exclude rows not containing variants.
+.TP
+\fB\-p\fR, \fB\-\-private\fR
+Print only rows where only the subset columns carry an alternate allele.
+.TP
+\fB\-r\fR, \fB\-\-replace\-with\-ref\fR
+Replace the excluded types with reference allele instead of dot.
+.TP
+\fB\-t\fR, \fB\-\-type\fR <list>
+Comma\-separated list of variant types to include: SNPs,indels.
+.TP
+\fB\-u\fR, \fB\-\-keep\-uncalled\fR
+Do not exclude rows without calls.
+.TP
+\fB\-h\fR, \-?, \fB\-\-help\fR
+This help message.
+.SH EXAMPLES
+.IP
+cat in.vcf | vcf\-subset \fB\-r\fR \fB\-t\fR indels \fB\-e\fR \fB\-c\fR SAMPLE1 > out.vcf
Copied: trunk/packages/vcftools/trunk/debian/mans/vcf-to-tab.1 (from rev 20508, trunk/packages/vcftools/trunk/debian/vcf-to-tab.1)
===================================================================
--- trunk/packages/vcftools/trunk/debian/mans/vcf-to-tab.1 (rev 0)
+++ trunk/packages/vcftools/trunk/debian/mans/vcf-to-tab.1 2015-11-16 14:36:54 UTC (rev 20509)
@@ -0,0 +1,14 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.40.4.
+.TH VCF-TO-TAB "1" "July 2011" "vcf-to-tab 0.1.5" "User Commands"
+.SH NAME
+vcf-to-tab \- convert to tabix
+.SH SYNOPSIS
+.B vcf-to-tab
+[\fIOPTIONS\fR] \fI< in.vcf > out.tab\fR
+.SH OPTIONS
+.TP
+\fB\-h\fR, \-?, \fB\-\-help\fR
+This help message.
+.TP
+\fB\-i\fR, \fB\-\-iupac\fR
+Use one\-letter IUPAC codes
Copied: trunk/packages/vcftools/trunk/debian/mans/vcf-tstv.1 (from rev 20508, trunk/packages/vcftools/trunk/debian/vcf-tstv.1)
===================================================================
--- trunk/packages/vcftools/trunk/debian/mans/vcf-tstv.1 (rev 0)
+++ trunk/packages/vcftools/trunk/debian/mans/vcf-tstv.1 2015-11-16 14:36:54 UTC (rev 20509)
@@ -0,0 +1,12 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.41.1.
+.TH VCF-TSTV "1" "February 2013" "vcf-tstv" "User Commands"
+.SH NAME
+vcf-tstv \- vcf-tstv
+.SH SYNOPSIS
+.B cat
+\fIfile.vcf | vcf-tstv\fR
+.SH OPTIONS
+.TP
+\fB\-h\fR, \-?, \fB\-\-help\fR
+This help message.
+.IP
Copied: trunk/packages/vcftools/trunk/debian/mans/vcf-validator.1 (from rev 20508, trunk/packages/vcftools/trunk/debian/vcf-validator.1)
===================================================================
--- trunk/packages/vcftools/trunk/debian/mans/vcf-validator.1 (rev 0)
+++ trunk/packages/vcftools/trunk/debian/mans/vcf-validator.1 2015-11-16 14:36:54 UTC (rev 20509)
@@ -0,0 +1,17 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.40.4.
+.TH VCF-VALIDATOR "1" "July 2011" "vcf-validator 0.1.5" "User Commands"
+.SH NAME
+vcf-validator \- validate VCF file
+.SH SYNOPSIS
+.B vcf-validator
+[\fIOPTIONS\fR] \fIfile.vcf.gz\fR
+.SH OPTIONS
+.TP
+\fB\-d\fR, \fB\-\-duplicates\fR
+Warn about duplicate positions.
+.TP
+\fB\-u\fR, \fB\-\-unique\-messages\fR
+Output all messages only once.
+.TP
+\fB\-h\fR, \-?, \fB\-\-help\fR
+This help message.
Copied: trunk/packages/vcftools/trunk/debian/mans/vcftools.1 (from rev 20508, trunk/packages/vcftools/trunk/debian/vcftools.1)
===================================================================
--- trunk/packages/vcftools/trunk/debian/mans/vcftools.1 (rev 0)
+++ trunk/packages/vcftools/trunk/debian/mans/vcftools.1 2015-11-16 14:36:54 UTC (rev 20509)
@@ -0,0 +1,472 @@
+.TH VCFTOOLS "1" "July 2011" "vcftools 0.1.5" "User Commands"
+.SH NAME
+vcftools \- analyse VCF files
+.SH SYNOPSIS
+.B vcftools \fR[\fIOPTIONS\fR]
+.SH DESCRIPTION
+The vcftools program is run from the command line. The interface is
+inspired by PLINK, and so should be largely familiar to users of that
+package. Commands take the following form:
+
+ vcftools \-\-vcf file1.vcf \-\-chr 20 \-\-freq
+
+The above command tells vcftools to read in the file file1.vcf, extract
+sites on chromosome 20, and calculate the allele frequency at each site.
+The resulting allele frequency estimates are stored in the output file,
+out.freq. As in the above example, output from vcftools is mainly sent to
+output files, as opposed to being shown on the screen.
+
+Note that some commands may only be available in the latest version of
+vcftools. To obtain the latest version, you should use SVN to checkout the
+latest code, as described on the home page.
+
+Also note that polyploid genotypes are not currently supported.
+
+.SS Basic Options
+.TP
+\fB\-\-vcf\fR <filename>
+This option defines the VCF file to be processed. The files need to be
+decompressed prior to use with vcftools. vcftools expects files in VCF
+format v4.0, a specification of which can be found here.
+.TP
+\fB\-\-gzvcf\fR <filename>
+This option can be used in place of the \-\-vcf option to read compressed
+(gzipped) VCF files directly. Note that this option can be quite slow when
+used with large files.
+.TP
+\fB\-\-out\fR <prefix>
+This option defines the output filename prefix for all files generated by
+vcftools. For example, if <prefix> is set to output_filename, then all
+output files will be of the form output_filename.*** . If this option is
+omitted, all output files will have the prefix 'out.'.
+
+.SS Site Filter Options
+
+.TP
+\fB\-\-chr\fR <chromosom>
+Only process sites with a chromosome identifier matching <chromosome>
+.TP
+\fB\-\-from\-bp\fR <integer>
+.TP
+\fB\-\-to\-bp\fR <integer>
+These options define the physical range of sites will be processed. Sites
+outside of this range will be excluded. These options can only be used in
+conjunction with \-\-chr.
+.TP
+\fB\-\-snp\fR <string>
+Include SNP(s) with matching ID. This command can be used multiple times
+in order to include more than one SNP.
+.TP
+\fB\-\-snps\fR <filename>
+Include a list of SNPs given in a file. The file should contain a list of
+SNP IDs, with one ID per line.
+.TP
+\fB\-\-exclude\fR <filename>
+Exclude a list of SNPs given in a file. The file should contain a list of
+SNP IDs, with one ID per line.
+.TP
+\fB\-\-positions\fR <filename>
+Include a set of sites on the basis of a list of positions. Each line of
+the input file should contain a (tab-separated) chromosome and position.
+The file should have a header line. Sites not included in the list are
+excluded.
+.TP
+\fB\-\-bed\fR <filename>
+.TP
+\fB\-\-exclude\-bed\fR <filename>
+Include or exclude a set of sites on the basis of a BED file. Only the
+first three columns (chrom, chromStart and chromEnd) are required. The
+BED file should have a header line.
+.TP
+\fB\-\-remove\-filtered\-all\fR
+.TP
+\fB\-\-remove\-filtered\fR <sting>
+.TP
+\fB\-\-keep\-filtered\fR <sting>
+These options are used to filter sites on the basis of their FILTER flag.
+The first option removes all sites with a FILTER flag. The second option
+can be used to exclude sites with a specific filter flag. The third option
+can be used to select sites on the basis of specific filter flags.
+The second and third options can be used multiple times to specify multiple
+FILTERs. The \-\-keep\-filtered option is applied before
+the \-\-remove\-filtered
+option.
+.TP
+\fB\-\-minQ\fR <float>
+Include only sites with Quality above this threshold.
+.TP
+\fB\-\-min\-meanDP\fR <float>
+.TP
+\fB\-\-max\-meanDP\fR <float>
+Include sites with mean Depth within the thresholds defined by these options.
+.TP
+\fB\-\-maf\fR <float>
+.TP
+\fB\-\-max\-maf\fR <float>
+Include only sites with Minor Allele Frequency within the specified range.
+.TP
+\fB\-\-non\-ref\-af\fR <float>
+.TP
+\fB\-\-max\-non\-ref\-af\fR <float>
+Include only sites with Non-Reference Allele Frequency within the specified
+range.
+.TP
+\fB\-\-hue\fR <float>
+Assesses sites for Hardy-Weinberg Equilibrium using an exact test, as
+defined by Wigginton, Cutler and Abecasis (2005). Sites with a p-value
+below the threshold defined by this option are taken to be out of HWE,
+and therefore excluded.
+.TP
+\fB\-\-geno\fR <float>
+Exclude sites on the basis of the proportion of missing data (defined to
+be between 0 and 1).
+.TP
+\fB\-\-min\-alleles\fR <int>
+.TP
+\fB\-\-max\-alleles\fR <int>
+Include only sites with a number of alleles within the specified range.
+For example, to include only bi\-allelic sites, one could use:
+
+ vcftools \-\-vcf file1.vcf \-\-min\-alleles 2 \-\-max\-alleles 2
+
+.TP
+\fB\-\-mask\fR <filename>
+.TP
+\fB\-\-invert\-mask\fR <filename>
+.TP
+\fB\-\-mask\-min\fR <filename>
+Include sites on the basis of a FASTA-like file. The provided file contains
+a sequence of integer digits (between 0 and 9) for each position on a
+chromosome that specify if a site at that position should be filtered or not.
+An example mask file would look like:
+
+ >1
+ 0000011111222...
+
+In this example, sites in the VCF file located within the first 5 bases of
+the start of chromosome 1 would be kept, whereas sites at position 6 onwards
+would be filtered out. The threshold integer that determines if sites are
+filtered or not is set using the \-\-mask\-min option, which defaults to 0.
+The chromosomes contained in the mask file must be sorted in the same order
+as the VCF file. The \-\-mask option is used to specify the mask file to be
+used, whereas the \-\-invert\-mask option can be used to specify a mask file
+that will be inverted before being applied.
+
+.SS Individual Filters
+
+.TP
+\fB\-\-indv\fR <string>
+Specify an individual to be kept in the analysis. This option can be used
+multiple times to specify multiple individuals.
+.TP
+\fB\-\-keep\fR <filename>
+Provide a file containing a list of individuals to include in subsequent a
+nalysis. Each individual ID (as defined in the VCF headerline) should be
+included on a separate line.
+.TP
+\fB\-\-remove\-indv\fR <string>
+Specify an individual to be removed from the analysis. This option can be
+used multiple times to specify multiple individuals. If the \-\-indv option
+is also specified, then the \-\-indv option is executed before
+the \-\-remove\-indv option.
+.TP
+\fB\-\-remove\fR <filename>
+Provide a file containing a list of individuals to exclude in subsequent
+analysis. Each individual ID (as defined in the VCF headerline) should be
+included on a separate line. If both the \-\-keep and the \-\-remove options
+are used, then the \-\-keep option is execute before the \-\-remove option.
+.TP
+\fB\-\-mon\-indv\-meanDP\fR <float>
+.TP
+\fB\-\-max\-indv\-meanDP\fR <float>
+Calculate the mean coverage on a per-individual basis. Only individuals with
+coverage within the range specified by these options are included in
+subsequent analyses.
+.TP
+\fB\-\-mind\fR <float>
+Specify the minimum call rate threshold for each individual.
+.TP
+\fB\-\-phased\fR
+First excludes all individuals having all genotypes unphased, and
+subsequently excludes all sites with unphased genotypes. The remaining data
+therefore consists of phased data only.
+
+.SS Genotype Filters
+.TP
+\fB\-\-remove\-filtered\-geno\-all\fR
+.TP
+\fB\-\-remove\-filtered\-geno\fR <string>
+The first option removes all genotypes with a FILTER flag. The second option
+can be used to exclude genotypes with a specific filter flag.
+.TP
+\fB\-\-minGQ\fR <float>
+Exclude all genotypes with a quality below the threshold specified by
+this option (GQ).
+.TP
+\fB\-\-minDP\fR <float>
+Exclude all genotypes with a sequencing depth below that specified by
+this option (DP)
+
+.SS Output Statistics
+.TP
+\fB\-\-freq\fR
+.TP
+\fB\-\-counts\fR
+.TP
+\fB\-\-freq2\fR
+.TP
+\fB\-\-counts2\fR
+Output per\-site frequency information. The \-\-freq outputs the allele
+frequency in a file with the suffix '.frq'. The \-\-counts option outputs a
+similar file with the suffix '.frq.count', that contains the raw allele
+counts at each site.
+The \-\-freq2 and \-\-count2 options are used to suppress allele information in
+the output file. In this case, the order of the freqs/counts depends on the
+numbering in the VCF file.
+.TP
+\fB\-\-depth\fR
+Generates a file containing the mean depth per individual. This file has
+the suffix '.idepth'.
+.TP
+\fB\-\-site\-depth\fR
+.TP
+\fB\-\-site\-mean\-depth\fR
+Generates a file containing the depth per site. The \-\-site\-depth option
+outputs the depth for each site summed across individuals. This file has
+the suffix '.ldepth'. Likewise, the \-\-site\-mean\-depth outputs the mean
+depth for each site, and the output file has the suffix '.ldepth.mean'.
+.TP
+\fB\-\-geno\-depth\fR
+Generates a (possibly very large) file containing the depth for each
+genotype in the VCF file. Missing entries are given the value \-1. The
+file has the suffix '.gdepth'.
+.TP
+\fB\-\-site\-quality\fR
+Generates a file containing the per\-site SNP quality, as found in the QUAL
+column of the VCF file. This file has the suffix '.lqual'.
+.TP
+\fB\-\-het\fR
+Calculates a measure of heterozygosity on a per\-individual basis.
+Specfically, the inbreeding coefficient, F, is estimated for each
+individual using a method of moments. The resulting file has the suffix '.het'.
+.TP
+\fB\-\-hardy\fR
+Reports a p\-value for each site from a Hardy\-Weinberg Equilibrium test
+(as defined by Wigginton, Cutler and Abecasis (2005)). The resulting file
+(with suffix '.hwe') also contains the Observed numbers of Homozygotes and
+Heterozygotes and the corresponding Expected numbers under HWE.
+.TP
+\fB\-\-missing\fR
+Generates two files reporting the missingness on a per\-individual and
+per\-site basis. The two files have suffixes '.imiss' and '.lmiss'
+respectively.
+.TP
+\fB\-\-hap\-r2\fR
+.TP
+\fB\-\-geno\-r2\fR
+.TP
+\fB\-\-ld\-window\fR <int>
+.TP
+\fB\-\-ld\-window\-bp\fR <int>
+.TP
+\fB\-\-min\-r2\fR <float>
+These options are used to report Linkage Disequilibrium (LD) statistics
+as summarised by the r2 statistic. The \-\-hap\-r2 option informs vcftools
+to output a file reporting the r2 statistic using phased haplotypes. This
+is the traditional measure of LD often reported in the population genetics
+literature. If phased haplotypes are unavailable then the \-\-geno\-r2 option
+may be used, which calculates the squared correlation coefficient between
+genotypes encoded as 0, 1 and 2 to represent the number of non-reference
+alleles in each individual. This is the same as the LD measure reported
+by PLINK. The haplotype version outputs a file with the suffix '.hap.ld',
+whereas the genotype version outputs a file with the suffix '.geno.ld'.
+The haplotype version implies the option \-\-phased.
+
+The \-\-ld\-window option defines the maximum SNP separation for the
+calculation of LD. Likewise, the \-\-ld\-window\-bp option can be used to
+define the maximum physical separation of SNPs included in the LD
+calculation. Finally, the \-\-min\-r2 sets a minimum value for r2 below
+which the LD statistic is not reported.
+.TP
+\fB\-\-SNPdnsity\fR <int>
+Calculates the number and density of SNPs in bins of size defined by this
+option. The resulting output file has the suffix '.snpden'.
+.TP
+\fB\-\-TsTv\fR <int>
+Calculates the Transition / Transversion ratio in bins of size defined by
+this option. The resulting output file has the suffix '.TsTv'. A summary
+is also supplied in a file with the suffix '.TsTv.summary'.
+.TP
+\fB\-\-FILTER\-summary\fR
+Generates a summary of the number of SNPs and Ts/Tv ratio for each FILTER
+category. The output file has the suffix '.FILTER.summary.
+.TP
+\fB\-\-filtered\-sites\fR
+Creates two files listing sites that have been kept or removed after
+filtering. The first file, with suffix '.kept.sites', lists sites kept
+by vcftools after filters have been applied. The second file, with the
+suffix '.removed.sites', list sites removed by the applied filters.
+.TP
+\fB\-\-singletons\fR
+This option will generate a file detailing the location of singletons, and
+the individual they occur in. The file reports both true singletons, and
+private doubletons (i.e. SNPs where the minor allele only occurs in a
+single individual and that individual is homozygotic for that allele).
+The output file has the suffix '.singletons'.
+.TP
+\fB\-\-site\-pi\fR
+.TP
+\fB\-\-window\-pi\fR <int>
+These options are used to estimate levels of nucleotide diversity. The first
+option does this on a per\-site basis, and the output file has the
+suffix '.sites.pi'. The second option calculates the nucleotide diversity in
+windows, with the window size defined in the option argument. Output for
+this option has the suffix '.windowed.pi'. The windowed version requires
+phased data, and hence use of this option implies the \-\-phased option.
+
+.SS Output in Other Formats
+.TP
+\fB\-\-O12\fR
+This option outputs the genotypes as a large matrix. Three files are
+produced. The first, with suffix '.012', contains the genotypes of each
+individual on a separate line. Genotypes are represented as 0, 1 and 2,
+where the number represent that number of non-reference alleles. Missing
+genotypes are represented by \-1. The second file, with suffix '.012.indv'
+details the individuals included in the main file. The third file, with
+suffix '.012.pos' details the site locations included in the main file.
+.TP
+\fB\-\-IMPUTE\fR
+This option outputs phased haplotypes in IMPUTE reference\-panel format. As
+IMPUTE requires phased data, using this option also implies \-\-phased.
+Unphased individuals and genotypes are therefore excluded. Only bi\-allelic
+sites are included in the output. Using this option generates three files.
+The IMPUTE haplotype file has the suffix '.impute.hap', and the IMPUTE
+legend file has the suffix '.impute.hap.legend'. The third file, with
+suffix '.impute.hap.indv', details the individuals included in the
+haplotype file, although this file is not needed by IMPUTE.
+.TP
+\fB\-\-ldhat\fR
+.TP
+\fB\-\-ldhat\-geno\fR
+These options output data in LDhat format. Use of these options also
+require the \-\-chr option to by used. The \-\-ldhat option outputs phased
+data only, and therefore also implies \-\-phased, leading to unphased
+individuals and genotypes being excluded. Alternatively, the \-\-ldhat\-geno
+option treats all of the data as unphased, and therefore outputs LDhat
+files in genotype/unphased format. In either case, two files are generated
+with the suffixes '.ldhat.sites' and '.ldhat.locs', which correspond to the
+LDhat 'sites' and 'locs' input files respectively.
+.TP
+\fB\-\-BEAGLE\-GL\fR
+This option outputs genotype likelihood information for input into the
+BEAGLE program. This option requires the VCF file to contain the FORMAT
+GL tag, which can generally be output by SNP callers such as the GATK.
+Use of this option requires a chromosome to be specified via the
+\-\-chr option. The resulting output file (with the suffix '.BEAGLE.GL')
+contains genotype likelihoods for biallelic sites, and is suitable for
+input into BEAGLE via the 'like=' argument.
+.TP
+\fB\-\-plink\fR
+This option outputs the genotype data in PLINK PED format. Two files are
+generated, with suffixes '.ped' and '.map'. Note that only bi\-allelic loci
+will be output. Further details of these files can be found in the PLINK
+documentation.
+
+Note: This option can be very slow on large datasets. Using the \-\-chr option
+to divide up the dataset is advised.
+.TP
+\fB\-\-plink\-tped\fR
+The \-\-plink option above can be extremely slow on large datasets. An
+alternative that might be considerably quicker is to output in the
+PLINK transposed format. This can be achieved using the \-\-plink\-tped
+option, which produces two files with suffixes '.tped' and '.tfam'.
+.TP
+\fB\-\-recode\fR
+The \-\-recode option is used to generate a VCF file from the input VCF file
+having applied the options specified by the user. The output file has the
+suffix '.recode.vcf'.
+
+By default, the INFO fields are removed from the output file, as the INFO
+values may be invalidated by the recoding (e.g. the total depth may need to
+be recalculated if individuals are removed). This default functionality can
+be overridden by using the \-\-keep\-INFO <string> option, where <string>
+defines the INFO key to keep in the output file. The \-\-keep\-INFO flag can
+be used multiple times. Alternatively, the option \-\-keep\-INFO-all can be
+used to retain all INFO fields.
+
+.SS Miscellaneous
+.TP
+\fB\-\-extract\-FORMAT\-info\fR <string>
+Extract information from the genotype fields in the VCF file relating to a
+specfied FORMAT identifier. For example, using the
+option '\-\-extract\-FORMAT\-info GT' would extract the all of the GT
+(i.e. Genotype)
+entries. The resulting output file has the suffix '.<FORMAT_ID>.FORMAT'.
+.TP
+\fB\-\-get\-INFO\fR <string>
+This option is used to extract information from the INFO field in the VCF
+file. The <string> argument specifies the INFO tag to be extracted, and the
+option can be used multiple times in order to extract multiple INFO entries.
+The resulting file, with suffix '.INFO', contains the required INFO
+information in a tab\-separated table. For example, to extract the NS and
+DB flags, one would use the command:
+
+ vcftools \-\-vcf file1.vcf \-\-get\-INFO NS \-\-get\-INFO DB
+
+.SS VCF File Comparison Options
+
+The file comparison options are currently in a state of flux and likely buggy.
+If you find a bug, please report it. Note that genotype\-level filters are not
+supported in these options.
+
+.TP
+\fB\-\-diff\fR <filename>
+.TP
+\fB\-\-gzdiff\fR <filename>
+Select a VCF file for comparison with the file specified by the \-\-vcf option.
+Outputs two files describing the sites and individuals common / unique to
+each file. These files have the suffixes '.diff.sites_in_files'
+and '.diff.indv_in_files' respectively. The \-\-gzdiff version can be used to
+read compressed VCF files.
+.TP
+\fB\-\-diff\-site\-discordance\fR
+Used in conjunction with the \-\-diff option to calculate discordance on a
+site by site basis. The resulting output file has the suffix '.diff.sites'.
+.TP
+\fB\-\-diff\-indv\-discordance\fR
+Used in conjunction with the \-\-diff option to calculate discordance on a
+per-individual basis. The resulting output file has the suffix '.diff.indv'.
+.TP
+\fB\-\-diff\-discordance\-matrix\fR
+Used in conjunction with the \-\-diff option to calculate a discordance matrix.
+This option only works with bi\-allelic loci with matching alleles that are
+present in both files. The resulting output file has the
+suffix '.diff.discordance.matrix'.
+.TP
+\fB\-\-diff\-switch\-error\fR
+Used in conjunction with the \-\-diff option to calculate phasing errors
+(specifically 'switch errors'). This option generates two output files
+describing switch errors found between sites, and the average switch error
+per individual. These two files have the suffixes '.diff.switch'
+and '.diff.indv.switch' respectively.
+
+.SS Options still in development
+
+The following options are yet to be finalised, are likely to contain bugs,
+and are likely to change in the future.
+.TP
+\fB\-\-fst\fR <filename>
+.TP
+\fB\-\-gzfst\fR <filename>
+Calculate FST for a pair of VCF files, with the second file being specified
+by this option. FST is currently calculated using the formula described in
+the supplementary material of the Phase I HapMap paper. Currently, only
+pairwise FST calculations are supported, although this will likely change
+in the future. The \-\-gzfst option can be used to read compressed VCF files.
+
+.TP
+\fB\-\-LROH\fR
+Identify Long Runs of Homozygosity.
+.TP
+\fB\-\-relatedness\fR
+Output Individual Relatedness Statistics.
Deleted: trunk/packages/vcftools/trunk/debian/vcf-annotate.1
===================================================================
--- trunk/packages/vcftools/trunk/debian/vcf-annotate.1 2015-11-16 14:23:28 UTC (rev 20508)
+++ trunk/packages/vcftools/trunk/debian/vcf-annotate.1 2015-11-16 14:36:54 UTC (rev 20509)
@@ -1,84 +0,0 @@
-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.40.4.
-.TH VCF-ANNOTATE "1" "July 2011" "vcf-annotate 0.1.5" "User Commands"
-.SH NAME
-vcf-annotate \- annotate VCF file, add filters or custom annotations
-.SH SYNOPSIS
-.B cat
-\fIin.vcf | vcf-annotate \fR[\fIOPTIONS\fR] \fI> out.vcf\fR
-.SH DESCRIPTION
-About: Annotates VCF file, adding filters or custom annotations. Requires tabix indexed file with annotations.
-.IP
-Currently annotates only the INFO column, but it will be extended on demand.
-.SH OPTIONS
-.TP
-\fB\-a\fR, \fB\-\-annotations\fR <file.gz>
-The tabix indexed file with the annotations: CHR\etFROM[\etTO][\etVALUE]+.
-.TP
-\fB\-c\fR, \fB\-\-columns\fR <list>
-The list of columns in the annotation file, e.g. CHROM,FROM,TO,\-,INFO/STR,INFO/GN. The dash
-in this example indicates that the third column should be ignored. If TO is not
-present, it is assumed that TO equals to FROM.
-.TP
-\fB\-d\fR, \fB\-\-description\fR <file|string>
-Header annotation, e.g. key=INFO,ID=HM2,Number=0,Type=Flag,Description='HapMap2 membership'.
-The descriptions can be read from a file, one annotation per line.
-.TP
-\fB\-f\fR, \fB\-\-filter\fR <list>
-Apply filters, list is in the format flt1=value/flt2/flt3=value/etc.
-.TP
-\fB\-h\fR, \-?, \fB\-\-help\fR
-This help message.
-.SS "Filters:"
-.TP
-+
-Apply all filters with default values (can be overridden, see the example below).
-.TP
-\fB\-X\fR
-Exclude the filter X
-.TP
-1, StrandBias
-FLOAT Min P\-value for strand bias (given PV4) [0.0001]
-.TP
-2, BaseQualBias
-FLOAT Min P\-value for baseQ bias [1e\-100]
-.TP
-3, MapQualBias
-FLOAT Min P\-value for mapQ bias [0]
-.TP
-4, EndDistBias
-FLOAT Min P\-value for end distance bias [0.0001]
-.TP
-a, MinAB
-INT Minimum number of alternate bases [2]
-.TP
-c, SnpCluster
-INT1,INT2 Filters clusters of 'INT1' or more SNPs within a run of 'INT2' bases []
-.TP
-D, MaxDP
-INT Maximum read depth [10000000]
-.TP
-d, MinDP
-INT Minimum read depth [2]
-.TP
-q, MinMQ
-INT Minimum RMS mapping quality for SNPs [10]
-.TP
-Q, Qual
-INT Minimum value of the QUAL field [10]
-.TP
-r, RefN
-Reference base is N []
-.TP
-W, GapWin
-INT Window size for filtering adjacent gaps [10]
-.TP
-w, SnpGap
-INT SNP within INT bp around a gap to be filtered [10]
-.SS "Example:"
-.IP
-zcat in.vcf.gz | vcf\-annotate \fB\-a\fR annotations.gz \fB\-d\fR descriptions.txt | bgzip \fB\-c\fR >out.vcf.gz
-zcat in.vcf.gz | vcf\-annotate \fB\-f\fR +/\-a/c=3,10/q=3/d=5/\-D \fB\-a\fR annotations.gz \fB\-d\fR descriptions.txt | bgzip \fB\-c\fR >out.vcf.gz
-.SS "Where descriptions.txt contains:"
-.IP
-key=INFO,ID=GN,Number=1,Type=String,Description='Gene Name'
-key=INFO,ID=STR,Number=1,Type=Integer,Description='Strand'
Deleted: trunk/packages/vcftools/trunk/debian/vcf-compare.1
===================================================================
--- trunk/packages/vcftools/trunk/debian/vcf-compare.1 2015-11-16 14:23:28 UTC (rev 20508)
+++ trunk/packages/vcftools/trunk/debian/vcf-compare.1 2015-11-16 14:36:54 UTC (rev 20509)
@@ -1,40 +0,0 @@
-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.40.4.
-.TH VCF-COMPARE "1" "July 2011" "vcf-compare 0.1.5" "User Commands"
-.SH NAME
-vcf-compare \- compare bgzipped and tabix indexed VCF files
-.SH SYNOPSIS
-.B compare-vcf
-[\fIOPTIONS\fR] \fIfile1.vcf file2.vcf \fR...
-.SH DESCRIPTION
-About: Compare bgzipped and tabix indexed VCF files. (E.g. bgzip file.vcf; tabix \fB\-p\fR vcf file.vcf.gz)
-.SH OPTIONS
-.TP
-\fB\-c\fR, \fB\-\-chromosomes\fR <list|file>
-Same as \fB\-r\fR, left for backward compatibility. Please do not use as it will be dropped in the future.
-.TP
-\fB\-d\fR, \fB\-\-debug\fR
-Debugging information. Giving the option multiple times increases verbosity
-.TP
-\fB\-H\fR, \fB\-\-cmp\-haplotypes\fR
-Compare haplotypes, not only positions
-.TP
-\fB\-m\fR, \fB\-\-name\-mapping\fR <list|file>
-Use with \fB\-H\fR when comparing files with differing column names. The argument to this options is a
-comma\-separated list or one mapping per line in a file. The names are colon separated and must
-appear in the same order as the files on the command line.
-.TP
-\fB\-R\fR, \fB\-\-refseq\fR <file>
-Compare the actual sequence, not just positions. Use with \fB\-w\fR to compare indels.
-.TP
-\fB\-r\fR, \fB\-\-regions\fR <list|file>
-Process the given regions (comma\-separated list or one region per line in a file).
-.TP
-\fB\-s\fR, \fB\-\-samples\fR <list>
-Process only the listed samples. Excluding unwanted samples may increase performance considerably.
-.TP
-\fB\-w\fR, \fB\-\-win\fR <int>
-In repetitive sequences, the same indel can be called at different positions. Consider
-records this far apart as matching (be it a SNP or an indel).
-.TP
-\fB\-h\fR, \-?, \fB\-\-help\fR
-This help message.
Deleted: trunk/packages/vcftools/trunk/debian/vcf-concat.1
===================================================================
--- trunk/packages/vcftools/trunk/debian/vcf-concat.1 2015-11-16 14:23:28 UTC (rev 20508)
+++ trunk/packages/vcftools/trunk/debian/vcf-concat.1 2015-11-16 14:36:54 UTC (rev 20509)
@@ -1,23 +0,0 @@
-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.40.4.
-.TH VCF-CONCAT "1" "July 2011" "vcf-concat 0.1.5" "User Commands"
-.SH NAME
-vcf-concat \- concatenate VCF files
-.SH SYNOPSIS
-.B vcf-concat
-[\fIOPTIONS\fR] \fIA.vcf.gz B.vcf.gz C.vcf.gz > out.vcf\fR
-.SH DESCRIPTION
-About: Convenience tool for concatenating VCF files. In the basic mode it does not
-.IP
-do anything fancy except for a sanity check that all files have the same columns.
-When run with the \fB\-s\fR option, it will perform a partial merge sort, looking at
-a limited number of open jobs simultaneously.
-.SH OPTIONS
-.TP
-\fB\-f\fR, \fB\-\-files\fR <file>
-Read the list of files from a file.
-.TP
-\fB\-s\fR, \fB\-\-merge\-sort\fR <int>
-Allow small overlaps in N consecutive files.
-.TP
-\fB\-h\fR, \-?, \fB\-\-help\fR
-This help message.
Deleted: trunk/packages/vcftools/trunk/debian/vcf-consensus.1
===================================================================
--- trunk/packages/vcftools/trunk/debian/vcf-consensus.1 2015-11-16 14:23:28 UTC (rev 20508)
+++ trunk/packages/vcftools/trunk/debian/vcf-consensus.1 2015-11-16 14:36:54 UTC (rev 20509)
@@ -1,14 +0,0 @@
-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.41.1.
-.TH VCF-CONSENSUS "1" "February 2013" "vcf-consensus" "User Commands"
-.SH NAME
-vcf-consensus \- vcf-consensus
-.SH SYNOPSIS
-.B cat
-\fIref.fa | vcf-consensus \fR[\fIOPTIONS\fR] \fIin.vcf.gz > out.txt\fR
-.SH OPTIONS
-.TP
-\fB\-h\fR, \-?, \fB\-\-help\fR
-This help message.
-.HP
-\fB\-s\fR, \fB\-\-sample\fR <name>
-.IP
Deleted: trunk/packages/vcftools/trunk/debian/vcf-contrast.1
===================================================================
--- trunk/packages/vcftools/trunk/debian/vcf-contrast.1 2015-11-16 14:23:28 UTC (rev 20508)
+++ trunk/packages/vcftools/trunk/debian/vcf-contrast.1 2015-11-16 14:36:54 UTC (rev 20509)
@@ -1,39 +0,0 @@
-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.41.1.
-.TH VCF-CONTRAST "1" "February 2013" "vcf-contrast" "User Commands"
-.SH NAME
-vcf-contrast \- finds differences amongst samples
-.SH SYNOPSIS
-.B vcf-contrast
-\fI+<list> -<list> \fR[\fIOPTIONS\fR] \fIfile.vcf.gz\fR
-.SH DESCRIPTION
-About: Finds differences amongst samples adding NOVEL* annotation to INFO field.
-.SH OPTIONS
-.TP
-+<list>
-List of samples where unique variant is expected
-.TP
-\-<list>
-List of background samples
-.TP
-\fB\-d\fR, \fB\-\-min\-DP\fR <int>
-Minimum depth across all \-<list> samples
-.TP
-\fB\-f\fR, \fB\-\-apply\-filters\fR
-Skip sites with FILTER column different from PASS or "."
-.TP
-\fB\-n\fR, \fB\-\-novel\-sites\fR
-Print only records with novel genotypes
-.TP
-\fB\-h\fR, \-?, \fB\-\-help\fR
-This help message.
-.SS "Example:"
-.IP
-# Test if any of the samples A,B is different from all C,D,E
-vcf\-contrast +A,B \fB\-C\fR,D,E \fB\-m\fR file.vcf.gz
-.IP
-# Same as above but printing only sites with novel variants and table output
-vcf\-contrast \fB\-n\fR +A,B \fB\-C\fR,D,E \fB\-m\fR file.vcf.gz | vcf\-query \fB\-f\fR '%CHROM %POS\et%INFO/NOVELTY\et%INFO/NOVELAL\et%INFO/NOVELGT[\et%SAMPLE %GTR %PL]\en'
-.IP
-# Similar to above but require minimum mapping quality of 20
-vcf\-annotate \fB\-f\fR MinMQ=20 file.vcf.gz | vcf\-contrast +A,B,C \fB\-D\fR,E,F \fB\-f\fR
-.IP
Deleted: trunk/packages/vcftools/trunk/debian/vcf-convert.1
===================================================================
--- trunk/packages/vcftools/trunk/debian/vcf-convert.1 2015-11-16 14:23:28 UTC (rev 20508)
+++ trunk/packages/vcftools/trunk/debian/vcf-convert.1 2015-11-16 14:36:54 UTC (rev 20509)
@@ -1,19 +0,0 @@
-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.40.4.
-.TH VCF-CONVERT "1" "July 2011" "vcf-convert 0.1.5" "User Commands"
-.SH NAME
-vcf-convert \- convert between VCF versions
-.SH SYNOPSIS
-.B cat
-\fIin.vcf | vcf-convert \fR[\fIOPTIONS\fR] \fI> out.vcf\fR
-.SH DESCRIPTION
-About: Convert between VCF versions, currently to VCFv4.0 only.
-.SH OPTIONS
-.TP
-\fB\-r\fR, \fB\-\-refseq\fR <file>
-The reference sequence in samtools faindexed fasta file. (Not required with SNPs only.)
-.TP
-\fB\-v\fR, \fB\-\-version\fR <string>
-4.0
-.TP
-\fB\-h\fR, \-?, \fB\-\-help\fR
-This help message.
Deleted: trunk/packages/vcftools/trunk/debian/vcf-fix-ploidy.1
===================================================================
--- trunk/packages/vcftools/trunk/debian/vcf-fix-ploidy.1 2015-11-16 14:23:28 UTC (rev 20508)
+++ trunk/packages/vcftools/trunk/debian/vcf-fix-ploidy.1 2015-11-16 14:36:54 UTC (rev 20509)
@@ -1,52 +0,0 @@
-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.41.1.
-.TH VCF-FIX-PLOIDY "1" "February 2013" "vcf-fix-ploidy" "User Commands"
-.SH NAME
-vcf-fix-ploidy \- vcf-fix-ploidy
-.SH SYNOPSIS
-.B cat
-\fIbroken.vcf | vcf-fix-ploidy \fR[\fIOPTIONS\fR] \fI> fixed.vcf\fR
-.SH OPTIONS
-.TP
-\fB\-a\fR, \fB\-\-assumed\-sex\fR <sex>
-M or F, required if the list is not complete in \fB\-s\fR
-.TP
-\fB\-l\fR, \fB\-\-fix\-likelihoods\fR
-Add or remove het likelihoods (not the default behaviour)
-.TP
-\fB\-p\fR, \fB\-\-ploidy\fR <file>
-Ploidy definition. The default is shown below.
-.TP
-\fB\-s\fR, \fB\-\-samples\fR <file>
-List of sample sexes (sample_name [MF]).
-.TP
-\fB\-h\fR, \-?, \fB\-\-help\fR
-This help message.
-.SS "Default ploidy definition:"
-.IP
-ploidy =>
-{
-.IP
-X =>
-[
-.IP
-# The pseudoautosomal regions 60,001\-2,699,520 and 154,931,044\-155,270,560 with the ploidy 2
-{ from=>1, to=>60_000, M=>1 },
-{ from=>2_699_521, to=>154_931_043, M=>1 },
-.IP
-],
-Y =>
-[
-.IP
-# No chrY in females and one copy in males
-{ from=>1, to=>59_373_566, M=>1, F=>0 },
-.IP
-],
-MT =>
-[
-.IP
-# Haploid MT in males and females
-{ from=>1, to => 16_569, M=>1, F=>1 },
-.IP
-],
-.IP
-}
Deleted: trunk/packages/vcftools/trunk/debian/vcf-indel-stats.1
===================================================================
--- trunk/packages/vcftools/trunk/debian/vcf-indel-stats.1 2015-11-16 14:23:28 UTC (rev 20508)
+++ trunk/packages/vcftools/trunk/debian/vcf-indel-stats.1 2015-11-16 14:36:54 UTC (rev 20509)
@@ -1,19 +0,0 @@
-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.41.1.
-.TH VCF-INDEL-STATS "1" "February 2013" "vcf-indel-stats" "User Commands"
-.SH NAME
-vcf-indel-stats \- vcf-indel-stat
-.SH SYNOPSIS
-.B vcf-indel-stats
-[\fIOPTIONS\fR] \fI< in.vcf > out.txt\fR
-.SH DESCRIPTION
-About: Currently calculates in\-frame ratio.
-.SH OPTIONS
-.TP
-\fB\-h\fR, \-?, \fB\-\-help\fR
-This help message.
-.TP
-\fB\-e\fR, \fB\-\-exons\fR <file>
-Tab\-separated file with exons (chr,from,to; 1\-based, inclusive)
-.HP
-\fB\-v\fR, \fB\-\-verbose\fR
-.IP
Deleted: trunk/packages/vcftools/trunk/debian/vcf-isec.1
===================================================================
--- trunk/packages/vcftools/trunk/debian/vcf-isec.1 2015-11-16 14:23:28 UTC (rev 20508)
+++ trunk/packages/vcftools/trunk/debian/vcf-isec.1 2015-11-16 14:36:54 UTC (rev 20509)
@@ -1,48 +0,0 @@
-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.40.4.
-.TH VCF-ISEC "1" "July 2011" "vcf-isec 0.1.5" "User Commands"
-.SH NAME
-vcf-isec \- create intersections, unions, complements on bgzipped and tabix indexed VCF or tab-delimited files
-.SH SYNOPSIS
-.B vcf-isec
-[\fIOPTIONS\fR] \fIfile1.vcf file2.vcf \fR...
-.SH DESCRIPTION
-About: Create intersections, unions, complements on bgzipped and tabix indexed VCF or tab\-delimited files.
-.IP
-Note that lines from all files can be intermixed together on the output, which can yield
-unexpected results.
-.SH OPTIONS
-.TP
-\fB\-C\fR, \fB\-\-chromosomes\fR <list|file>
-Process the given chromosomes (comma\-separated list or one chromosome per line in a file).
-.TP
-\fB\-c\fR, \fB\-\-complement\fR
-Output positions present in the first file but missing from the other files.
-.TP
-\fB\-d\fR, \fB\-\-debug\fR
-Debugging information
-.TP
-\fB\-f\fR, \fB\-\-force\fR
-Continue even if the script complains about differing columns.
-.TP
-\fB\-o\fR, \fB\-\-one\-file\-only\fR
-Print only entries from the left\-most file. Without \fB\-o\fR, all unique positions will be printed.
-.TP
-\fB\-n\fR, \fB\-\-nfiles\fR [+\-=]<int>
-Output positions present in this many (=), this many or more (+), or this many or fewer (\-) files.
-.TP
-\fB\-p\fR, \fB\-\-prefix\fR <path>
-If present, multiple files will be created with all possible isec combinations. (Suitable for Venn Diagram analysis.)
-.TP
-\fB\-t\fR, \fB\-\-tab\fR <chr:pos:file>
-Tab\-delimited file with indexes of chromosome and position columns. (1\-based indexes)
-.TP
-\fB\-w\fR, \fB\-\-win\fR <int>
-In repetitive sequences, the same indel can be called at different positions. Consider
-records this far apart as matching (be it a SNP or an indel).
-.TP
-\fB\-h\fR, \-?, \fB\-\-help\fR
-This help message.
-.SH EXAMPLES
-.IP
-bgzip file.vcf; tabix \fB\-p\fR vcf file.vcf.gz
-bgzip file.tab; tabix \fB\-s\fR 1 \fB\-b\fR 2 \fB\-e\fR 2 file.tab.gz
Deleted: trunk/packages/vcftools/trunk/debian/vcf-merge.1
===================================================================
--- trunk/packages/vcftools/trunk/debian/vcf-merge.1 2015-11-16 14:23:28 UTC (rev 20508)
+++ trunk/packages/vcftools/trunk/debian/vcf-merge.1 2015-11-16 14:36:54 UTC (rev 20509)
@@ -1,28 +0,0 @@
-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.40.4.
-.TH VCF-MERGE "1" "July 2011" "vcf-merge 0.1.5" "User Commands"
-.SH NAME
-vcf-merge \- merge the bgzipped and tabix indexed VCF files
-.SH SYNOPSIS
-.B merge-vcf
-[\fIOPTIONS\fR] \fIfile1.vcf file2.vcf.gz \fR... \fI> out.vcf\fR
-.SH DESCRIPTION
-About: Merge the bgzipped and tabix indexed VCF files. (E.g. bgzip file.vcf; tabix \fB\-p\fR vcf file.vcf.gz)
-.SH OPTIONS
-.TP
-\fB\-c\fR, \fB\-\-chromosomes\fR <list|file>
-Same as \fB\-r\fR, left for backward compatibility. Please do not use as it will be dropped in the future.
-.TP
-\fB\-d\fR, \fB\-\-remove\-duplicates\fR
-If there should be two consecutive rows with the same chr:pos, print only the first one.
-.TP
-\fB\-H\fR, \fB\-\-vcf\-header\fR <file>
-Use the VCF header
-.TP
-\fB\-h\fR, \-?, \fB\-\-help\fR
-This help message.
-.TP
-\fB\-r\fR, \fB\-\-regions\fR <list|file>
-Do only the given regions (comma\-separated list or one region per line in a file).
-.TP
-\fB\-s\fR, \fB\-\-silent\fR
-Try to be a bit more silent, no warnings about duplicate lines.
Deleted: trunk/packages/vcftools/trunk/debian/vcf-phased-join.1
===================================================================
--- trunk/packages/vcftools/trunk/debian/vcf-phased-join.1 2015-11-16 14:23:28 UTC (rev 20508)
+++ trunk/packages/vcftools/trunk/debian/vcf-phased-join.1 2015-11-16 14:36:54 UTC (rev 20509)
@@ -1,28 +0,0 @@
-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.41.1.
-.TH VCF-PHASED-JOIN "1" "February 2013" "vcf-phased-join" "User Commands"
-.SH NAME
-vcf-phased-join \- take multiple overlapping pre\-phased chunks and concatenates them into one VCF
-.SH SYNOPSIS
-.B vcf-phased-join
-[\fIOPTIONS\fR] \fIA.vcf B.vcf C.vcf\fR
-.SH DESCRIPTION
-About: The script takes multiple overlapping pre\-phased chunks and concatenates them into one VCF
-.IP
-using heterozygous calls from the overlaps to determine correct phase.
-.SH OPTIONS
-.TP
-\fB\-j\fR, \fB\-\-min\-join\-quality\fR <num>
-Quality threshold for gluing the pre\-phased blocks together [10]
-.TP
-\fB\-l\fR, \fB\-\-list\fR <file>
-List of VCFs to join.
-.TP
-\fB\-o\fR, \fB\-\-output\fR <file>
-Output file name. When "\-" is supplied, STDOUT and STDERR will be used
-.TP
-\fB\-q\fR, \fB\-\-min\-PQ\fR <num>
-Break pre\-phased segments if PQ value is lower in input VCFs [0.6]
-.TP
-\fB\-h\fR, \-?, \fB\-\-help\fR
-This help message
-.IP
Deleted: trunk/packages/vcftools/trunk/debian/vcf-query.1
===================================================================
--- trunk/packages/vcftools/trunk/debian/vcf-query.1 2015-11-16 14:23:28 UTC (rev 20508)
+++ trunk/packages/vcftools/trunk/debian/vcf-query.1 2015-11-16 14:36:54 UTC (rev 20509)
@@ -1,29 +0,0 @@
-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.40.4.
-.TH VCF-QUERY "1" "July 2011" "vcf-query 0.1.5" "User Commands"
-.SH NAME
-vcf-query \- query VCF files
-.SH SYNOPSIS
-.B query-vcf
-[\fIOPTIONS\fR] \fIfile.vcf.gz\fR
-.SH OPTIONS
-.TP
-\fB\-c\fR, \fB\-\-columns\fR <NA001,NA002,..>
-List of comma\-separated column names.
-.TP
-\fB\-f\fR, \fB\-\-format\fR <string>
-The default is '%CHROM:%POS\et%REF[\et%SAMPLE=%GT]\en'
-.TP
-\fB\-l\fR, \fB\-\-list\-columns\fR
-List columns.
-.TP
-\fB\-r\fR, \fB\-\-region\fR chr:from\-to
-Retrieve the region. (Runs tabix.)
-.TP
-\fB\-h\fR, \-?, \fB\-\-help\fR
-This help message.
-.SH EXAMPLES
-.IP
-query\-vcf file.vcf.gz 1:1000\-2000 \fB\-c\fR NA001,NA002,NA003
-query\-vcf file.vcf.gz \fB\-r\fR 1:1000\-2000 \fB\-f\fR '%CHROM:%POS\et%REF[\et%SAMPLE:%*=,]\en'
-query\-vcf file.vcf.gz \fB\-f\fR '[%GT\et]%LINE\en'
-query\-vcf file.vcf.gz \fB\-f\fR '%CHROM\et%POS\et%INFO/DP\et%FILTER\en'
Deleted: trunk/packages/vcftools/trunk/debian/vcf-shuffle-cols.1
===================================================================
--- trunk/packages/vcftools/trunk/debian/vcf-shuffle-cols.1 2015-11-16 14:23:28 UTC (rev 20508)
+++ trunk/packages/vcftools/trunk/debian/vcf-shuffle-cols.1 2015-11-16 14:36:54 UTC (rev 20509)
@@ -1,17 +0,0 @@
-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.41.1.
-.TH VCF-SHUFFLE-COLS "1" "February 2013" "vcf-shuffle-cols" "User Commands"
-.SH NAME
-vcf-shuffle-cols \- reorder columns
-.SH SYNOPSIS
-.B vcf-shuffle-cols
-[\fIOPTIONS\fR] \fI-t template.vcf.gz file.vcf.gz > out.vcf\fR
-.SH DESCRIPTION
-About: Reorder columns to match the order in the template VCF.
-.SH OPTIONS
-.TP
-\fB\-t\fR, \fB\-\-template\fR <file>
-The file with the correct order of the columns.
-.TP
-\fB\-h\fR, \-?, \fB\-\-help\fR
-This help message.
-.IP
Deleted: trunk/packages/vcftools/trunk/debian/vcf-sort.1
===================================================================
--- trunk/packages/vcftools/trunk/debian/vcf-sort.1 2015-11-16 14:23:28 UTC (rev 20508)
+++ trunk/packages/vcftools/trunk/debian/vcf-sort.1 2015-11-16 14:36:54 UTC (rev 20509)
@@ -1,14 +0,0 @@
-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.40.4.
-.TH VCF-SORT "1" "July 2011" "vcf-sort 0.1.5" "User Commands"
-.SH NAME
-vcf-sort \- sort VCF file
-.SH SYNOPSIS
-.B vcf-sort
-\fI> out.vcf\fR
-.SH DESCRIPTION
-.IP
-cat file.vcf | vcf\-sort > out.vcf
-.SH OPTIONS
-.TP
-\fB\-h\fR, \-?, \fB\-\-help\fR
-This help message.
Deleted: trunk/packages/vcftools/trunk/debian/vcf-stats.1
===================================================================
--- trunk/packages/vcftools/trunk/debian/vcf-stats.1 2015-11-16 14:23:28 UTC (rev 20508)
+++ trunk/packages/vcftools/trunk/debian/vcf-stats.1 2015-11-16 14:36:54 UTC (rev 20509)
@@ -1,35 +0,0 @@
-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.40.4.
-.TH VCF-STATS "1" "July 2011" "vcf-stats 0.1.5" "User Commands"
-.SH NAME
-vcf-stats \- statistic of VCF file
-.SH SYNOPSIS
-.B vcf-stats
-[\fIOPTIONS\fR] \fIfile.vcf.gz\fR
-.SH OPTIONS
-.TP
-\fB\-d\fR, \fB\-\-dump\fR <file>
-Take an existing dump file and recreate the files (works with \fB\-p\fR)
-.TP
-\fB\-f\fR, \fB\-\-filters\fR <filter1,filter2>
-List of filters such as column/field (any value), column/field=bin:max (cluster in bins),column/field=value (exact value)
-.TP
-\fB\-p\fR, \fB\-\-prefix\fR <dir/string>
-Prefix of output files. If slashes are present, directories will be created.
-.TP
-\fB\-s\fR, \fB\-\-samples\fR <list>
-Process only the listed samples, \- for none. Excluding unwanted samples may increase performance considerably.
-.TP
-\fB\-h\fR, \-?, \fB\-\-help\fR
-This help message.
-.SH EXAMPLES
-.IP
-# Calculate stats separately for the filter field, quality and non\-indels
-vcf\-stats file.vcf.gz \fB\-f\fR FILTER,QUAL=10:200,INFO/INDEL=False \fB\-p\fR out/
-.IP
-# Calculate stats for all samples
-vcf\-stats file.vcf.gz \fB\-f\fR FORMAT/DP=10:200 \fB\-p\fR out/
-.IP
-# Calculate stats only for the sample NA00001
-vcf\-stats file.vcf.gz \fB\-f\fR SAMPLE/NA00001/DP=1:200 \fB\-p\fR out/
-.IP
-vcf\-stats file.vcf.gz > perl.dump
Deleted: trunk/packages/vcftools/trunk/debian/vcf-subset.1
===================================================================
--- trunk/packages/vcftools/trunk/debian/vcf-subset.1 2015-11-16 14:23:28 UTC (rev 20508)
+++ trunk/packages/vcftools/trunk/debian/vcf-subset.1 2015-11-16 14:36:54 UTC (rev 20509)
@@ -1,32 +0,0 @@
-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.40.4.
-.TH VCF-SUBSET "1" "July 2011" "vcf-subset 0.1.5" "User Commands"
-.SH NAME
-vcf-subset \- create subset of VCF file
-.SH SYNOPSIS
-.B vcf-subset
-[\fIOPTIONS\fR] \fIin.vcf.gz > out.vcf\fR
-.SH OPTIONS
-.TP
-\fB\-c\fR, \fB\-\-columns\fR <string>
-File or comma\-separated list of columns to keep in the vcf file. If file, one column per row
-.TP
-\fB\-e\fR, \fB\-\-exclude\-ref\fR
-Exclude rows not containing variants.
-.TP
-\fB\-p\fR, \fB\-\-private\fR
-Print only rows where only the subset columns carry an alternate allele.
-.TP
-\fB\-r\fR, \fB\-\-replace\-with\-ref\fR
-Replace the excluded types with reference allele instead of dot.
-.TP
-\fB\-t\fR, \fB\-\-type\fR <list>
-Comma\-separated list of variant types to include: SNPs,indels.
-.TP
-\fB\-u\fR, \fB\-\-keep\-uncalled\fR
-Do not exclude rows without calls.
-.TP
-\fB\-h\fR, \-?, \fB\-\-help\fR
-This help message.
-.SH EXAMPLES
-.IP
-cat in.vcf | vcf\-subset \fB\-r\fR \fB\-t\fR indels \fB\-e\fR \fB\-c\fR SAMPLE1 > out.vcf
Deleted: trunk/packages/vcftools/trunk/debian/vcf-to-tab.1
===================================================================
--- trunk/packages/vcftools/trunk/debian/vcf-to-tab.1 2015-11-16 14:23:28 UTC (rev 20508)
+++ trunk/packages/vcftools/trunk/debian/vcf-to-tab.1 2015-11-16 14:36:54 UTC (rev 20509)
@@ -1,14 +0,0 @@
-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.40.4.
-.TH VCF-TO-TAB "1" "July 2011" "vcf-to-tab 0.1.5" "User Commands"
-.SH NAME
-vcf-to-tab \- convert to tabix
-.SH SYNOPSIS
-.B vcf-to-tab
-[\fIOPTIONS\fR] \fI< in.vcf > out.tab\fR
-.SH OPTIONS
-.TP
-\fB\-h\fR, \-?, \fB\-\-help\fR
-This help message.
-.TP
-\fB\-i\fR, \fB\-\-iupac\fR
-Use one\-letter IUPAC codes
Deleted: trunk/packages/vcftools/trunk/debian/vcf-tstv.1
===================================================================
--- trunk/packages/vcftools/trunk/debian/vcf-tstv.1 2015-11-16 14:23:28 UTC (rev 20508)
+++ trunk/packages/vcftools/trunk/debian/vcf-tstv.1 2015-11-16 14:36:54 UTC (rev 20509)
@@ -1,12 +0,0 @@
-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.41.1.
-.TH VCF-TSTV "1" "February 2013" "vcf-tstv" "User Commands"
-.SH NAME
-vcf-tstv \- vcf-tstv
-.SH SYNOPSIS
-.B cat
-\fIfile.vcf | vcf-tstv\fR
-.SH OPTIONS
-.TP
-\fB\-h\fR, \-?, \fB\-\-help\fR
-This help message.
-.IP
Deleted: trunk/packages/vcftools/trunk/debian/vcf-validator.1
===================================================================
--- trunk/packages/vcftools/trunk/debian/vcf-validator.1 2015-11-16 14:23:28 UTC (rev 20508)
+++ trunk/packages/vcftools/trunk/debian/vcf-validator.1 2015-11-16 14:36:54 UTC (rev 20509)
@@ -1,17 +0,0 @@
-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.40.4.
-.TH VCF-VALIDATOR "1" "July 2011" "vcf-validator 0.1.5" "User Commands"
-.SH NAME
-vcf-validator \- validate VCF file
-.SH SYNOPSIS
-.B vcf-validator
-[\fIOPTIONS\fR] \fIfile.vcf.gz\fR
-.SH OPTIONS
-.TP
-\fB\-d\fR, \fB\-\-duplicates\fR
-Warn about duplicate positions.
-.TP
-\fB\-u\fR, \fB\-\-unique\-messages\fR
-Output all messages only once.
-.TP
-\fB\-h\fR, \-?, \fB\-\-help\fR
-This help message.
Deleted: trunk/packages/vcftools/trunk/debian/vcftools.1
===================================================================
--- trunk/packages/vcftools/trunk/debian/vcftools.1 2015-11-16 14:23:28 UTC (rev 20508)
+++ trunk/packages/vcftools/trunk/debian/vcftools.1 2015-11-16 14:36:54 UTC (rev 20509)
@@ -1,472 +0,0 @@
-.TH VCFTOOLS "1" "July 2011" "vcftools 0.1.5" "User Commands"
-.SH NAME
-vcftools \- analyse VCF files
-.SH SYNOPSIS
-.B vcftools \fR[\fIOPTIONS\fR]
-.SH DESCRIPTION
-The vcftools program is run from the command line. The interface is
-inspired by PLINK, and so should be largely familiar to users of that
-package. Commands take the following form:
-
- vcftools \-\-vcf file1.vcf \-\-chr 20 \-\-freq
-
-The above command tells vcftools to read in the file file1.vcf, extract
-sites on chromosome 20, and calculate the allele frequency at each site.
-The resulting allele frequency estimates are stored in the output file,
-out.freq. As in the above example, output from vcftools is mainly sent to
-output files, as opposed to being shown on the screen.
-
-Note that some commands may only be available in the latest version of
-vcftools. To obtain the latest version, you should use SVN to checkout the
-latest code, as described on the home page.
-
-Also note that polyploid genotypes are not currently supported.
-
-.SS Basic Options
-.TP
-\fB\-\-vcf\fR <filename>
-This option defines the VCF file to be processed. The files need to be
-decompressed prior to use with vcftools. vcftools expects files in VCF
-format v4.0, a specification of which can be found here.
-.TP
-\fB\-\-gzvcf\fR <filename>
-This option can be used in place of the \-\-vcf option to read compressed
-(gzipped) VCF files directly. Note that this option can be quite slow when
-used with large files.
-.TP
-\fB\-\-out\fR <prefix>
-This option defines the output filename prefix for all files generated by
-vcftools. For example, if <prefix> is set to output_filename, then all
-output files will be of the form output_filename.*** . If this option is
-omitted, all output files will have the prefix 'out.'.
-
-.SS Site Filter Options
-
-.TP
-\fB\-\-chr\fR <chromosom>
-Only process sites with a chromosome identifier matching <chromosome>
-.TP
-\fB\-\-from\-bp\fR <integer>
-.TP
-\fB\-\-to\-bp\fR <integer>
-These options define the physical range of sites will be processed. Sites
-outside of this range will be excluded. These options can only be used in
-conjunction with \-\-chr.
-.TP
-\fB\-\-snp\fR <string>
-Include SNP(s) with matching ID. This command can be used multiple times
-in order to include more than one SNP.
-.TP
-\fB\-\-snps\fR <filename>
-Include a list of SNPs given in a file. The file should contain a list of
-SNP IDs, with one ID per line.
-.TP
-\fB\-\-exclude\fR <filename>
-Exclude a list of SNPs given in a file. The file should contain a list of
-SNP IDs, with one ID per line.
-.TP
-\fB\-\-positions\fR <filename>
-Include a set of sites on the basis of a list of positions. Each line of
-the input file should contain a (tab-separated) chromosome and position.
-The file should have a header line. Sites not included in the list are
-excluded.
-.TP
-\fB\-\-bed\fR <filename>
-.TP
-\fB\-\-exclude\-bed\fR <filename>
-Include or exclude a set of sites on the basis of a BED file. Only the
-first three columns (chrom, chromStart and chromEnd) are required. The
-BED file should have a header line.
-.TP
-\fB\-\-remove\-filtered\-all\fR
-.TP
-\fB\-\-remove\-filtered\fR <sting>
-.TP
-\fB\-\-keep\-filtered\fR <sting>
-These options are used to filter sites on the basis of their FILTER flag.
-The first option removes all sites with a FILTER flag. The second option
-can be used to exclude sites with a specific filter flag. The third option
-can be used to select sites on the basis of specific filter flags.
-The second and third options can be used multiple times to specify multiple
-FILTERs. The \-\-keep\-filtered option is applied before
-the \-\-remove\-filtered
-option.
-.TP
-\fB\-\-minQ\fR <float>
-Include only sites with Quality above this threshold.
-.TP
-\fB\-\-min\-meanDP\fR <float>
-.TP
-\fB\-\-max\-meanDP\fR <float>
-Include sites with mean Depth within the thresholds defined by these options.
-.TP
-\fB\-\-maf\fR <float>
-.TP
-\fB\-\-max\-maf\fR <float>
-Include only sites with Minor Allele Frequency within the specified range.
-.TP
-\fB\-\-non\-ref\-af\fR <float>
-.TP
-\fB\-\-max\-non\-ref\-af\fR <float>
-Include only sites with Non-Reference Allele Frequency within the specified
-range.
-.TP
-\fB\-\-hue\fR <float>
-Assesses sites for Hardy-Weinberg Equilibrium using an exact test, as
-defined by Wigginton, Cutler and Abecasis (2005). Sites with a p-value
-below the threshold defined by this option are taken to be out of HWE,
-and therefore excluded.
-.TP
-\fB\-\-geno\fR <float>
-Exclude sites on the basis of the proportion of missing data (defined to
-be between 0 and 1).
-.TP
-\fB\-\-min\-alleles\fR <int>
-.TP
-\fB\-\-max\-alleles\fR <int>
-Include only sites with a number of alleles within the specified range.
-For example, to include only bi\-allelic sites, one could use:
-
- vcftools \-\-vcf file1.vcf \-\-min\-alleles 2 \-\-max\-alleles 2
-
-.TP
-\fB\-\-mask\fR <filename>
-.TP
-\fB\-\-invert\-mask\fR <filename>
-.TP
-\fB\-\-mask\-min\fR <filename>
-Include sites on the basis of a FASTA-like file. The provided file contains
-a sequence of integer digits (between 0 and 9) for each position on a
-chromosome that specify if a site at that position should be filtered or not.
-An example mask file would look like:
-
- >1
- 0000011111222...
-
-In this example, sites in the VCF file located within the first 5 bases of
-the start of chromosome 1 would be kept, whereas sites at position 6 onwards
-would be filtered out. The threshold integer that determines if sites are
-filtered or not is set using the \-\-mask\-min option, which defaults to 0.
-The chromosomes contained in the mask file must be sorted in the same order
-as the VCF file. The \-\-mask option is used to specify the mask file to be
-used, whereas the \-\-invert\-mask option can be used to specify a mask file
-that will be inverted before being applied.
-
-.SS Individual Filters
-
-.TP
-\fB\-\-indv\fR <string>
-Specify an individual to be kept in the analysis. This option can be used
-multiple times to specify multiple individuals.
-.TP
-\fB\-\-keep\fR <filename>
-Provide a file containing a list of individuals to include in subsequent a
-nalysis. Each individual ID (as defined in the VCF headerline) should be
-included on a separate line.
-.TP
-\fB\-\-remove\-indv\fR <string>
-Specify an individual to be removed from the analysis. This option can be
-used multiple times to specify multiple individuals. If the \-\-indv option
-is also specified, then the \-\-indv option is executed before
-the \-\-remove\-indv option.
-.TP
-\fB\-\-remove\fR <filename>
-Provide a file containing a list of individuals to exclude in subsequent
-analysis. Each individual ID (as defined in the VCF headerline) should be
-included on a separate line. If both the \-\-keep and the \-\-remove options
-are used, then the \-\-keep option is execute before the \-\-remove option.
-.TP
-\fB\-\-mon\-indv\-meanDP\fR <float>
-.TP
-\fB\-\-max\-indv\-meanDP\fR <float>
-Calculate the mean coverage on a per-individual basis. Only individuals with
-coverage within the range specified by these options are included in
-subsequent analyses.
-.TP
-\fB\-\-mind\fR <float>
-Specify the minimum call rate threshold for each individual.
-.TP
-\fB\-\-phased\fR
-First excludes all individuals having all genotypes unphased, and
-subsequently excludes all sites with unphased genotypes. The remaining data
-therefore consists of phased data only.
-
-.SS Genotype Filters
-.TP
-\fB\-\-remove\-filtered\-geno\-all\fR
-.TP
-\fB\-\-remove\-filtered\-geno\fR <string>
-The first option removes all genotypes with a FILTER flag. The second option
-can be used to exclude genotypes with a specific filter flag.
-.TP
-\fB\-\-minGQ\fR <float>
-Exclude all genotypes with a quality below the threshold specified by
-this option (GQ).
-.TP
-\fB\-\-minDP\fR <float>
-Exclude all genotypes with a sequencing depth below that specified by
-this option (DP)
-
-.SS Output Statistics
-.TP
-\fB\-\-freq\fR
-.TP
-\fB\-\-counts\fR
-.TP
-\fB\-\-freq2\fR
-.TP
-\fB\-\-counts2\fR
-Output per\-site frequency information. The \-\-freq outputs the allele
-frequency in a file with the suffix '.frq'. The \-\-counts option outputs a
-similar file with the suffix '.frq.count', that contains the raw allele
-counts at each site.
-The \-\-freq2 and \-\-count2 options are used to suppress allele information in
-the output file. In this case, the order of the freqs/counts depends on the
-numbering in the VCF file.
-.TP
-\fB\-\-depth\fR
-Generates a file containing the mean depth per individual. This file has
-the suffix '.idepth'.
-.TP
-\fB\-\-site\-depth\fR
-.TP
-\fB\-\-site\-mean\-depth\fR
-Generates a file containing the depth per site. The \-\-site\-depth option
-outputs the depth for each site summed across individuals. This file has
-the suffix '.ldepth'. Likewise, the \-\-site\-mean\-depth outputs the mean
-depth for each site, and the output file has the suffix '.ldepth.mean'.
-.TP
-\fB\-\-geno\-depth\fR
-Generates a (possibly very large) file containing the depth for each
-genotype in the VCF file. Missing entries are given the value \-1. The
-file has the suffix '.gdepth'.
-.TP
-\fB\-\-site\-quality\fR
-Generates a file containing the per\-site SNP quality, as found in the QUAL
-column of the VCF file. This file has the suffix '.lqual'.
-.TP
-\fB\-\-het\fR
-Calculates a measure of heterozygosity on a per\-individual basis.
-Specfically, the inbreeding coefficient, F, is estimated for each
-individual using a method of moments. The resulting file has the suffix '.het'.
-.TP
-\fB\-\-hardy\fR
-Reports a p\-value for each site from a Hardy\-Weinberg Equilibrium test
-(as defined by Wigginton, Cutler and Abecasis (2005)). The resulting file
-(with suffix '.hwe') also contains the Observed numbers of Homozygotes and
-Heterozygotes and the corresponding Expected numbers under HWE.
-.TP
-\fB\-\-missing\fR
-Generates two files reporting the missingness on a per\-individual and
-per\-site basis. The two files have suffixes '.imiss' and '.lmiss'
-respectively.
-.TP
-\fB\-\-hap\-r2\fR
-.TP
-\fB\-\-geno\-r2\fR
-.TP
-\fB\-\-ld\-window\fR <int>
-.TP
-\fB\-\-ld\-window\-bp\fR <int>
-.TP
-\fB\-\-min\-r2\fR <float>
-These options are used to report Linkage Disequilibrium (LD) statistics
-as summarised by the r2 statistic. The \-\-hap\-r2 option informs vcftools
-to output a file reporting the r2 statistic using phased haplotypes. This
-is the traditional measure of LD often reported in the population genetics
-literature. If phased haplotypes are unavailable then the \-\-geno\-r2 option
-may be used, which calculates the squared correlation coefficient between
-genotypes encoded as 0, 1 and 2 to represent the number of non-reference
-alleles in each individual. This is the same as the LD measure reported
-by PLINK. The haplotype version outputs a file with the suffix '.hap.ld',
-whereas the genotype version outputs a file with the suffix '.geno.ld'.
-The haplotype version implies the option \-\-phased.
-
-The \-\-ld\-window option defines the maximum SNP separation for the
-calculation of LD. Likewise, the \-\-ld\-window\-bp option can be used to
-define the maximum physical separation of SNPs included in the LD
-calculation. Finally, the \-\-min\-r2 sets a minimum value for r2 below
-which the LD statistic is not reported.
-.TP
-\fB\-\-SNPdnsity\fR <int>
-Calculates the number and density of SNPs in bins of size defined by this
-option. The resulting output file has the suffix '.snpden'.
-.TP
-\fB\-\-TsTv\fR <int>
-Calculates the Transition / Transversion ratio in bins of size defined by
-this option. The resulting output file has the suffix '.TsTv'. A summary
-is also supplied in a file with the suffix '.TsTv.summary'.
-.TP
-\fB\-\-FILTER\-summary\fR
-Generates a summary of the number of SNPs and Ts/Tv ratio for each FILTER
-category. The output file has the suffix '.FILTER.summary.
-.TP
-\fB\-\-filtered\-sites\fR
-Creates two files listing sites that have been kept or removed after
-filtering. The first file, with suffix '.kept.sites', lists sites kept
-by vcftools after filters have been applied. The second file, with the
-suffix '.removed.sites', list sites removed by the applied filters.
-.TP
-\fB\-\-singletons\fR
-This option will generate a file detailing the location of singletons, and
-the individual they occur in. The file reports both true singletons, and
-private doubletons (i.e. SNPs where the minor allele only occurs in a
-single individual and that individual is homozygotic for that allele).
-The output file has the suffix '.singletons'.
-.TP
-\fB\-\-site\-pi\fR
-.TP
-\fB\-\-window\-pi\fR <int>
-These options are used to estimate levels of nucleotide diversity. The first
-option does this on a per\-site basis, and the output file has the
-suffix '.sites.pi'. The second option calculates the nucleotide diversity in
-windows, with the window size defined in the option argument. Output for
-this option has the suffix '.windowed.pi'. The windowed version requires
-phased data, and hence use of this option implies the \-\-phased option.
-
-.SS Output in Other Formats
-.TP
-\fB\-\-O12\fR
-This option outputs the genotypes as a large matrix. Three files are
-produced. The first, with suffix '.012', contains the genotypes of each
-individual on a separate line. Genotypes are represented as 0, 1 and 2,
-where the number represent that number of non-reference alleles. Missing
-genotypes are represented by \-1. The second file, with suffix '.012.indv'
-details the individuals included in the main file. The third file, with
-suffix '.012.pos' details the site locations included in the main file.
-.TP
-\fB\-\-IMPUTE\fR
-This option outputs phased haplotypes in IMPUTE reference\-panel format. As
-IMPUTE requires phased data, using this option also implies \-\-phased.
-Unphased individuals and genotypes are therefore excluded. Only bi\-allelic
-sites are included in the output. Using this option generates three files.
-The IMPUTE haplotype file has the suffix '.impute.hap', and the IMPUTE
-legend file has the suffix '.impute.hap.legend'. The third file, with
-suffix '.impute.hap.indv', details the individuals included in the
-haplotype file, although this file is not needed by IMPUTE.
-.TP
-\fB\-\-ldhat\fR
-.TP
-\fB\-\-ldhat\-geno\fR
-These options output data in LDhat format. Use of these options also
-require the \-\-chr option to by used. The \-\-ldhat option outputs phased
-data only, and therefore also implies \-\-phased, leading to unphased
-individuals and genotypes being excluded. Alternatively, the \-\-ldhat\-geno
-option treats all of the data as unphased, and therefore outputs LDhat
-files in genotype/unphased format. In either case, two files are generated
-with the suffixes '.ldhat.sites' and '.ldhat.locs', which correspond to the
-LDhat 'sites' and 'locs' input files respectively.
-.TP
-\fB\-\-BEAGLE\-GL\fR
-This option outputs genotype likelihood information for input into the
-BEAGLE program. This option requires the VCF file to contain the FORMAT
-GL tag, which can generally be output by SNP callers such as the GATK.
-Use of this option requires a chromosome to be specified via the
-\-\-chr option. The resulting output file (with the suffix '.BEAGLE.GL')
-contains genotype likelihoods for biallelic sites, and is suitable for
-input into BEAGLE via the 'like=' argument.
-.TP
-\fB\-\-plink\fR
-This option outputs the genotype data in PLINK PED format. Two files are
-generated, with suffixes '.ped' and '.map'. Note that only bi\-allelic loci
-will be output. Further details of these files can be found in the PLINK
-documentation.
-
-Note: This option can be very slow on large datasets. Using the \-\-chr option
-to divide up the dataset is advised.
-.TP
-\fB\-\-plink\-tped\fR
-The \-\-plink option above can be extremely slow on large datasets. An
-alternative that might be considerably quicker is to output in the
-PLINK transposed format. This can be achieved using the \-\-plink\-tped
-option, which produces two files with suffixes '.tped' and '.tfam'.
-.TP
-\fB\-\-recode\fR
-The \-\-recode option is used to generate a VCF file from the input VCF file
-having applied the options specified by the user. The output file has the
-suffix '.recode.vcf'.
-
-By default, the INFO fields are removed from the output file, as the INFO
-values may be invalidated by the recoding (e.g. the total depth may need to
-be recalculated if individuals are removed). This default functionality can
-be overridden by using the \-\-keep\-INFO <string> option, where <string>
-defines the INFO key to keep in the output file. The \-\-keep\-INFO flag can
-be used multiple times. Alternatively, the option \-\-keep\-INFO-all can be
-used to retain all INFO fields.
-
-.SS Miscellaneous
-.TP
-\fB\-\-extract\-FORMAT\-info\fR <string>
-Extract information from the genotype fields in the VCF file relating to a
-specfied FORMAT identifier. For example, using the
-option '\-\-extract\-FORMAT\-info GT' would extract the all of the GT
-(i.e. Genotype)
-entries. The resulting output file has the suffix '.<FORMAT_ID>.FORMAT'.
-.TP
-\fB\-\-get\-INFO\fR <string>
-This option is used to extract information from the INFO field in the VCF
-file. The <string> argument specifies the INFO tag to be extracted, and the
-option can be used multiple times in order to extract multiple INFO entries.
-The resulting file, with suffix '.INFO', contains the required INFO
-information in a tab\-separated table. For example, to extract the NS and
-DB flags, one would use the command:
-
- vcftools \-\-vcf file1.vcf \-\-get\-INFO NS \-\-get\-INFO DB
-
-.SS VCF File Comparison Options
-
-The file comparison options are currently in a state of flux and likely buggy.
-If you find a bug, please report it. Note that genotype\-level filters are not
-supported in these options.
-
-.TP
-\fB\-\-diff\fR <filename>
-.TP
-\fB\-\-gzdiff\fR <filename>
-Select a VCF file for comparison with the file specified by the \-\-vcf option.
-Outputs two files describing the sites and individuals common / unique to
-each file. These files have the suffixes '.diff.sites_in_files'
-and '.diff.indv_in_files' respectively. The \-\-gzdiff version can be used to
-read compressed VCF files.
-.TP
-\fB\-\-diff\-site\-discordance\fR
-Used in conjunction with the \-\-diff option to calculate discordance on a
-site by site basis. The resulting output file has the suffix '.diff.sites'.
-.TP
-\fB\-\-diff\-indv\-discordance\fR
-Used in conjunction with the \-\-diff option to calculate discordance on a
-per-individual basis. The resulting output file has the suffix '.diff.indv'.
-.TP
-\fB\-\-diff\-discordance\-matrix\fR
-Used in conjunction with the \-\-diff option to calculate a discordance matrix.
-This option only works with bi\-allelic loci with matching alleles that are
-present in both files. The resulting output file has the
-suffix '.diff.discordance.matrix'.
-.TP
-\fB\-\-diff\-switch\-error\fR
-Used in conjunction with the \-\-diff option to calculate phasing errors
-(specifically 'switch errors'). This option generates two output files
-describing switch errors found between sites, and the average switch error
-per individual. These two files have the suffixes '.diff.switch'
-and '.diff.indv.switch' respectively.
-
-.SS Options still in development
-
-The following options are yet to be finalised, are likely to contain bugs,
-and are likely to change in the future.
-.TP
-\fB\-\-fst\fR <filename>
-.TP
-\fB\-\-gzfst\fR <filename>
-Calculate FST for a pair of VCF files, with the second file being specified
-by this option. FST is currently calculated using the formula described in
-the supplementary material of the Phase I HapMap paper. Currently, only
-pairwise FST calculations are supported, although this will likely change
-in the future. The \-\-gzfst option can be used to read compressed VCF files.
-
-.TP
-\fB\-\-LROH\fR
-Identify Long Runs of Homozygosity.
-.TP
-\fB\-\-relatedness\fR
-Output Individual Relatedness Statistics.
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