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changeset 0:ae1b0fbd53e8 draft default tip

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Imported from capsule None
author devteam
date Mon, 28 Jul 2014 11:30:07 -0400
parents
children
files test-data/vcf2pgSnp_input.vcf test-data/vcf2pgSnp_output.pgSnp vcf2pgSnp.pl vcf2pgSnp.xml
diffstat 4 files changed, 267 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/vcf2pgSnp_input.vcf	Mon Jul 28 11:30:07 2014 -0400
@@ -0,0 +1,50 @@
+##fileformat=VCFv4.1
+##INFO=<ID=LDAF,Number=1,Type=Float,Description="MLE Allele Frequency Accounting for LD">
+##INFO=<ID=AVGPOST,Number=1,Type=Float,Description="Average posterior probability from MaCH/Thunder">
+##INFO=<ID=RSQ,Number=1,Type=Float,Description="Genotype imputation quality from MaCH/Thunder">
+##INFO=<ID=ERATE,Number=1,Type=Float,Description="Per-marker Mutation rate from MaCH/Thunder">
+##INFO=<ID=THETA,Number=1,Type=Float,Description="Per-marker Transition rate from MaCH/Thunder">
+##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END for imprecise variants">
+##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS for imprecise variants">
+##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
+##INFO=<ID=HOMLEN,Number=.,Type=Integer,Description="Length of base pair identical micro-homology at event breakpoints">
+##INFO=<ID=HOMSEQ,Number=.,Type=String,Description="Sequence of base pair identical micro-homology at event breakpoints">
+##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="Difference in length between REF and ALT alleles">
+##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
+##INFO=<ID=AC,Number=.,Type=Integer,Description="Alternate Allele Count">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total Allele Count">
+##ALT=<ID=DEL,Description="Deletion">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=DS,Number=1,Type=Float,Description="Genotype dosage from MaCH/Thunder">
+##FORMAT=<ID=GL,Number=.,Type=Float,Description="Genotype Likelihoods">
+##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele, ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/pilot_data/technical/reference/ancestral_alignments/README">
+##INFO=<ID=AF,Number=1,Type=Float,Description="Global Allele Frequency based on AC/AN">
+##INFO=<ID=AMR_AF,Number=1,Type=Float,Description="Allele Frequency for samples from AMR based on AC/AN">
+##INFO=<ID=ASN_AF,Number=1,Type=Float,Description="Allele Frequency for samples from ASN based on AC/AN">
+##INFO=<ID=AFR_AF,Number=1,Type=Float,Description="Allele Frequency for samples from AFR based on AC/AN">
+##INFO=<ID=EUR_AF,Number=1,Type=Float,Description="Allele Frequency for samples from EUR based on AC/AN">
+##INFO=<ID=VT,Number=1,Type=String,Description="indicates what type of variant the line represents">
+##INFO=<ID=SNPSOURCE,Number=.,Type=String,Description="indicates if a snp was called when analysing the low coverage or exome alignment data">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	HG00096	HG00097	HG00099	HG00100
+1	10523	.	TCCG	T	152	PASS	VT=INDEL;RSQ=0.5246;ERATE=0.0023;AN=2184;AA=.;THETA=0.0172;AC=5;AVGPOST=0.9954;LDAF=0.0045;AF=0.00;AMR_AF=0.00;AFR_AF=0.01	GT:DS:GL	0|0:0.000:0.00,-1.50,-34.60	0|0:0.000:0.00,-0.90,-20.70	0|0:0.000:0.00,-1.50,-34.50	0|0:0.000:0.00,-0.30,-6.90
+1	10583	rs58108140	G	A	100	PASS	VT=SNP;SNPSOURCE=LOWCOV;AN=2184;AC=327;LDAF=0.2363;AVGPOST=0.7630;ERATE=0.0098;AA=.;RSQ=0.4161;THETA=0.0197;SNPSOURCE=LOWCOV;AF=0.15;ASN_AF=0.15;AMR_AF=0.18;AFR_AF=0.04;EUR_AF=0.21	GT:DS:GL	0|0:0.250:-0.18,-0.47,-2.42	0|0:0.200:-0.24,-0.44,-1.16	0|0:0.250:-0.15,-0.54,-3.12	0|1:0.750:-0.48,-0.48,-0.48
+1	10611	rs189107123	C	G	100	PASS	VT=SNP;SNPSOURCE=LOWCOV;THETA=0.0048;RSQ=0.3814;AN=2184;AVGPOST=0.9427;ERATE=0.0024;LDAF=0.0420;AA=.;SNPSOURCE=LOWCOV;AC=39;AF=0.02;ASN_AF=0.02;AMR_AF=0.02;AFR_AF=0.01;EUR_AF=0.02	GT:DS:GL	0|0:0.050:-0.48,-0.48,-0.48	0|0:0.350:-0.24,-0.44,-1.16	0|0:0.100:-0.22,-0.42,-1.80	0|0:0.100:-0.48,-0.48,-0.48
+1	10616	.	CCGCCGTTGCAAAGGCGCGCCG	C	2781	PASS	VT=INDEL;RSQ=0.1048;AN=2184;LDAF=0.7052;AVGPOST=0.5674;ERATE=0.0146;AA=.;THETA=0.0195;AC=1972;AF=0.90;ASN_AF=0.88;AMR_AF=0.92;AFR_AF=0.89;EUR_AF=0.92	GT:DS:GL	1|1:1.450:0,0,0	1|1:1.750:0,0,0	1|1:1.200:0,0,0	0|1:1.150:0,0,0
+1	11540	.	T	TA	263	PASS	VT=INDEL;AVGPOST=0.5915;LDAF=0.2676;AN=2184;RSQ=0.0831;AC=93;THETA=0.0011;AA=.;ERATE=0.0222;AF=0.04;ASN_AF=0.05;AMR_AF=0.04;AFR_AF=0.05;EUR_AF=0.04	GT:DS:GL	0|0:0.700:0,0,0	0|1:0.800:0,0,0	0|0:0.300:0,0,0	0|0:0.450:0,0,0
+1	13302	rs180734498	C	T	100	PASS	VT=SNP;SNPSOURCE=LOWCOV;THETA=0.0159;LDAF=0.1562;AN=2184;AC=250;AA=.;RSQ=0.6272;ERATE=0.0116;SNPSOURCE=LOWCOV;AVGPOST=0.8877;AF=0.11;ASN_AF=0.02;AMR_AF=0.09;AFR_AF=0.21;EUR_AF=0.13	GT:DS:GL	0|0:0.250:-0.13,-0.58,-3.62	0|1:0.950:-2.45,-0.00,-5.00	0|0:0.450:-0.29,-0.32,-5.00	0|0:0.300:-0.48,-0.48,-0.48
+1	13327	rs144762171	G	C	100	PASS	VT=SNP;SNPSOURCE=LOWCOV;RSQ=0.6776;THETA=0.0189;AN=2184;AC=57;AA=.;LDAF=0.0342;AVGPOST=0.9733;SNPSOURCE=LOWCOV;ERATE=0.0007;AF=0.03;ASN_AF=0.01;AMR_AF=0.03;AFR_AF=0.02;EUR_AF=0.04	GT:DS:GL	0|0:0.000:-0.03,-1.11,-5.00	0|1:1.000:-1.97,-0.01,-2.51	0|0:0.050:-0.01,-1.69,-5.00	0|0:0.100:-0.48,-0.48,-0.48
+1	13417	.	C	CGAGA	2788	PASS	VT=INDEL;AVGPOST=0.7560;THETA=0.0061;AC=52;AN=2184;AA=.;RSQ=0.1970;LDAF=0.1542;ERATE=0.0127;AF=0.02;ASN_AF=0.02;AMR_AF=0.04;AFR_AF=0.01;EUR_AF=0.03	GT:DS:GL	0|0:0.050:0.00,-0.30,-5.60	0|0:0.250:0,0,0	0|0:0.400:0,0,0	0|0:0.350:0.00,-0.30,-5.60
+1	13957	.	TC	T	226	PASS	VT=INDEL;RSQ=0.2600;AN=2184;AA=.;LDAF=0.0542;THETA=0.0144;AVGPOST=0.9144;ERATE=0.0029;AC=27;AF=0.01;ASN_AF=0.01;AMR_AF=0.01;AFR_AF=0.01;EUR_AF=0.01	GT:DS:GL	0|0:0.150:0,0,0	0|0:0.050:0,0,0	0|0:0.100:0,0,0	0|0:0.100:0,0,0
+1	13980	rs151276478	T	C	100	PASS	VT=SNP;SNPSOURCE=LOWCOV;ERATE=0.0021;THETA=0.0096;RSQ=0.3995;AN=2184;AC=55;LDAF=0.0628;AVGPOST=0.9128;AA=.;SNPSOURCE=LOWCOV;AF=0.03;ASN_AF=0.02;AMR_AF=0.03;AFR_AF=0.01;EUR_AF=0.03	GT:DS:GL	0|0:0.100:-0.48,-0.48,-0.48	0|1:0.950:-0.48,-0.48,-0.48	0|0:0.050:-0.48,-0.48,-0.48	0|0:0.050:-0.48,-0.48,-0.48
+1	16226	.	AG	A	104	PASS	VT=INDEL;THETA=0.0211;AN=2184;RSQ=0.6096;LDAF=0.0034;AVGPOST=0.9971;AA=A;ERATE=0.0008;AC=4;AF=0.00;AMR_AF=0.00;EUR_AF=0.00	GT:DS:GL	0|0:0.000:0.00,-1.50,-24.00	0|0:0.050:0,0,0	0|0:0.000:0.00,-0.30,-4.80	0|0:0.000:0.00,-0.90,-14.40
+1	17496	.	AC	A	209	PASS	VT=INDEL;AC=7;AN=2184;ERATE=0.0009;AA=A;RSQ=0.7057;THETA=0.0221;AVGPOST=0.9968;LDAF=0.0045;AF=0.00;AFR_AF=0.01	GT:DS:GL	0|0:0.000:0.00,-3.30,-42.90	0|0:0.000:0,0,0	0|0:0.000:0,0,0	0|0:0.000:0,0,0
+1	18869	.	ACC	A	126	PASS	VT=INDEL;LDAF=0.2562;AC=52;AN=2184;ERATE=0.0162;AVGPOST=0.5962;AA=A;RSQ=0.0889;THETA=0.0107;AF=0.02;ASN_AF=0.04;AMR_AF=0.02;AFR_AF=0.02;EUR_AF=0.01	GT:DS:GL	0|0:0.400:0,0,0	0|0:0.350:0,0,0	0|0:0.250:0.00,-0.30,-2.90	0|0:0.550:0,0,0
+1	19083	.	G	GCA	139	PASS	VT=INDEL;AVGPOST=0.7121;AN=2184;AC=13;AA=G;THETA=0.0077;ERATE=0.0123;RSQ=0.0826;LDAF=0.1645;AF=0.01;ASN_AF=0.01;AMR_AF=0.01;AFR_AF=0.01;EUR_AF=0.00	GT:DS:GL	0|0:0.200:0,0,0	0|0:0.400:0,0,0	0|0:0.250:0,0,0	0|0:0.350:0,0,0
+1	19190	.	GC	G	815	PASS	VT=INDEL;AC=131;LDAF=0.2531;AN=2184;AA=G;THETA=0.0161;AVGPOST=0.6408;RSQ=0.1696;ERATE=0.0188;AF=0.06;ASN_AF=0.05;AMR_AF=0.10;AFR_AF=0.07;EUR_AF=0.04	GT:DS:GL	0|0:0.650:0,0,0	0|0:0.200:0,0,0	0|0:0.650:0,0,0	0|0:0.500:0,0,0
+1	20862	.	A	AG	78	PASS	VT=INDEL;ERATE=0.0067;AVGPOST=0.8007;RSQ=0.0827;LDAF=0.8907;AN=2184;THETA=0.0095;AA=A;AC=2178;AF=1.00;ASN_AF=1.00;AMR_AF=1.00;AFR_AF=0.99;EUR_AF=1.00	GT:DS:GL	1|1:1.750:0,0,0	1|1:1.800:0,0,0	1|1:1.850:0,0,0	1|1:1.750:0,0,0
+1	30923	rs140337953	G	T	100	PASS	VT=SNP;SNPSOURCE=LOWCOV;RSQ=0.5363;LDAF=0.6540;THETA=0.0078;AN=2184;AA=T;ERATE=0.0127;AC=1581;SNPSOURCE=LOWCOV;AVGPOST=0.7309;AF=0.72;ASN_AF=0.88;AMR_AF=0.81;AFR_AF=0.48;EUR_AF=0.72	GT:DS:GL	1|1:1.950:-5.00,-0.61,-0.12	0|0:0.450:-0.10,-0.69,-2.81	0|0:0.450:-0.11,-0.64,-3.49	1|1:1.500:-0.48,-0.48,-0.48
+1	46402	.	C	CTGT	104	PASS	VT=INDEL;RSQ=0.0943;AA=C;AN=2184;AVGPOST=0.8697;THETA=0.0108;AC=5;LDAF=0.0697;ERATE=0.0056;AF=0.00;ASN_AF=0.00;AMR_AF=0.00;AFR_AF=0.01	GT:DS:GL	0|0:0.050:0,0,0	0|0:0.100:0,0,0	0|0:0.050:0,0,0	0|0:0.050:0,0,0
+1	47190	.	G	GA	868	PASS	VT=INDEL;LDAF=0.2298;AN=2184;AC=45;AA=G;RSQ=0.1035;AVGPOST=0.6322;THETA=0.0141;ERATE=0.0127;AF=0.02;ASN_AF=0.00;AMR_AF=0.03;AFR_AF=0.05;EUR_AF=0.01	GT:DS:GL	0|0:0.350:0,0,0	0|0:0.500:0,0,0	0|0:0.550:0,0,0	0|0:0.400:0,0,0
+1	49514	.	AG	A	449	PASS	VT=INDEL;THETA=0.0164;AC=52;AN=2184;RSQ=0.4892;AA=A;LDAF=0.0469;AVGPOST=0.9448;ERATE=0.0053;AF=0.02;ASN_AF=0.02;AMR_AF=0.02;AFR_AF=0.01;EUR_AF=0.03	GT:DS:GL	0|0:0.000:0.00,-0.90,-12.40	0|1:0.800:0,0,0	0|0:0.150:-0.10,0.00,0.00	0|0:0.000:0.00,-0.30,-4.20
+1	49515	.	G	GA	44	PASS	VT=INDEL;THETA=0.0214;AN=2184;AC=13;AA=A;ERATE=0.0008;AVGPOST=0.9879;LDAF=0.0111;RSQ=0.5361;AF=0.01;ASN_AF=0.02;EUR_AF=0.01	GT:DS:GL	0|0:0.050:0.00,-0.90,-9.70	0|0:0.050:0,0,0	0|0:0.000:0,0,0	0|0:0.000:0.00,-0.30,-3.20
+1	50481	.	GGT	G	2370	PASS	VT=INDEL;RSQ=0.3702;THETA=0.0038;AN=2184;AA=G;ERATE=0.0177;AVGPOST=0.7981;AC=142;LDAF=0.1660;AF=0.07;ASN_AF=0.05;AMR_AF=0.13;AFR_AF=0.07;EUR_AF=0.04	GT:DS:GL	0|0:0.250:0,0,0	0|0:0.350:0,0,0	1|0:1.150:-3.00,-0.30,0.00	0|0:0.250:0,0,0
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/vcf2pgSnp_output.pgSnp	Mon Jul 28 11:30:07 2014 -0400
@@ -0,0 +1,22 @@
+chr1	10522	10523	TCCG	1	8	0
+chr1	10582	10583	G/A	2	7,1	0,0
+chr1	10610	10611	C	1	8	0
+chr1	10615	10616	CCGCCGTTGCAAAGGCGCGCCG/C	2	1,7	0,0
+chr1	11539	11540	T/T	2	7,1	0,0
+chr1	13301	13302	C/T	2	7,1	0,0
+chr1	13326	13327	G/C	2	7,1	0,0
+chr1	13416	13417	C	1	8	0
+chr1	13956	13957	TC	1	8	0
+chr1	13979	13980	T/C	2	7,1	0,0
+chr1	16225	16226	AG	1	8	0
+chr1	17495	17496	AC	1	8	0
+chr1	18868	18869	ACC	1	8	0
+chr1	19082	19083	G	1	8	0
+chr1	19189	19190	GC	1	8	0
+chr1	20861	20862	A	1	8	0
+chr1	30922	30923	G/T	2	4,4	0,0
+chr1	46401	46402	C	1	8	0
+chr1	47189	47190	G	1	8	0
+chr1	49513	49514	AG/A	2	7,1	0,0
+chr1	49514	49515	G	1	8	0
+chr1	50480	50481	GGT/G	2	7,1	0,0
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/vcf2pgSnp.pl	Mon Jul 28 11:30:07 2014 -0400
@@ -0,0 +1,116 @@
+#!/usr/bin/perl -w
+use strict;
+
+#convert from a vcf file to a pgSnp file. 
+#frequency count = chromosome count
+#either a single column/individual 
+#or all columns as a population 
+
+my $in;
+my $stCol = 9;
+my $endCol;
+if (@ARGV && scalar @ARGV == 2) {
+   $stCol = shift @ARGV;
+   $in = shift @ARGV;
+   if ($stCol eq 'all') { $stCol = 10; }
+   else { $endCol = $stCol; }
+   $stCol--; #go from 1 based to zero based column number
+   if ($stCol < 9) { 
+      print "ERROR genotype fields don't start until column 10\n";
+      exit;
+   }
+}elsif (@ARGV && scalar @ARGV == 1) {
+   $in = shift @ARGV;
+}elsif (@ARGV) {
+   print "usage: vcf2pgSnp.pl [indColNum default=all] file.vcf > file.pgSnp\n";
+   exit;
+}
+
+open(FH, $in) or die "Couldn't open $in, $!\n";
+while (<FH>) {
+   chomp; 
+   if (/^\s*#/) { next; } #skip comments/headers
+   if (/^\s*$/) { next; } #skip blank lines
+   my @f = split(/\t/);
+   #chr pos1base ID refNt altNt[,|D#|Int] quality filter info format geno1 ...
+   my $a;
+   my %nt;
+   my %all;
+   my $cnt = 0;
+   my $var;
+   if ($f[3] eq 'N') { next; } #ignore ref=N
+   if ($f[4] =~ /[DI]/ or $f[3] =~ /[DI]/) { next; } #don't do microsatellite
+   #if ($f[4] =~ /[ACTG],[ACTG]/) { next; } #only do positions with single alternate
+   if ($f[6] && !($f[6] eq '.' or $f[6] eq 'PASS')) { next; } #filtered for some reason
+   my $ind = 0;
+   if ($f[8] ne 'GT') { #more than just genotype
+      my @t = split(/:/, $f[8]);
+      foreach (@t) { if ($_ eq 'GT') { last; } $ind++; }
+      if ($ind == 0 && $f[8] !~ /^GT/) { die "ERROR couldn't find genotype in format $f[8]\n"; }
+   }
+   #count 0's, 1's, 2's
+   if (!$endCol) { $endCol = $#f; }
+   foreach my $col ($stCol .. $endCol) {
+      if ($ind > 0) { 
+         my @t = split(/:/, $f[$col]);
+         $f[$col] = $t[$ind] . ":"; #only keep genotype part
+      }
+      if ($f[$col] =~ /^(0|1|2).(0|1|2)/) {
+         $nt{$1}++;
+         $nt{$2}++;
+      }elsif ($f[$col] =~ /^(0|1|2):/) { #chrY or male chrX, single
+         $nt{$1}++;
+      } #else ignore
+   }
+   if (%nt) {
+      if ($f[0] !~ /chr/) { $f[0] = "chr$f[0]"; }
+      print "$f[0]\t", ($f[1]-1), "\t$f[1]\t"; #position info
+      my $cnt = scalar(keys %nt);
+      my $fr;
+      my $sc;
+      my $all;
+      if (exists $nt{0}) {
+         $all = uc($f[3]);
+         $fr = $nt{0};
+         $sc = 0;
+      }
+      if (!exists $nt{0} && exists $nt{1}) {
+         if ($f[4] =~ /([ACTG]),?/) {
+            $all = $1;
+            $fr = $nt{1};
+            $sc = 0;
+         }else { die "bad variant nt $f[4] for nt 1"; }
+      }elsif (exists $nt{1}) {
+         if ($f[4] =~ /([ACTG]),?/) {
+            $all .= '/' . $1;
+            $fr .= ",$nt{1}";
+            $sc .= ",0";
+         }else { die "bad variant nt $f[4] for nt 1"; }
+      }
+      if (exists $nt{2}) {
+         if ($f[4] =~ /^[ACTG],([ACTG]),?/) {
+            $all .= '/' . $1;
+            $fr .= ",$nt{2}";
+            $sc .= ",0";
+         }else { die "bad variant nt $f[4] for nt 2"; }
+      }
+      if (exists $nt{3}) {
+         if ($f[4] =~ /^[ACTG],[ACTG],([ACTG])/) {
+            $all .= '/' . $1;
+            $fr .= ",$nt{3}";
+            $sc .= ",0";
+         }else { die "bad variant nt $f[4] for nt 3"; }
+      }
+      if (exists $nt{4}) {
+         if ($f[4] =~ /^[ACTG],[ACTG],[ACTG],([ACTG])/) {
+            $all .= '/' . $1;
+            $fr .= ",$nt{4}";
+            $sc .= ",0";
+         }else { die "bad variant nt $f[4] for nt 4"; }
+      }
+      print "$all\t$cnt\t$fr\t$sc\n";
+   }
+}
+close FH;
+
+exit;
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/vcf2pgSnp.xml	Mon Jul 28 11:30:07 2014 -0400
@@ -0,0 +1,79 @@
+<tool id="vcf2pgSnp" name="VCF to pgSnp" hidden="false" version="1.0.0">
+  <description>Convert from VCF to pgSnp format</description>
+  <command interpreter="perl">
+    #if $inType.how == "all" #vcf2pgSnp.pl all $input1 > $out_file1
+    #else #vcf2pgSnp.pl $inType.ind_column $input1 > $out_file1
+    #end if
+  </command>
+  <inputs>
+    <param format="vcf" name="input1" type="data" label="VCF dataset" />
+    <conditional name="inType">
+      <param name="how" type="select" label="How to treat individuals">
+        <option value="all">Group all as a population</option>
+        <option value="one">Do just one individual</option>
+      </param>
+      <when value="one">
+        <param name="ind_column" type="data_column" data_ref="input1" label="Column to convert" value="10" />
+      </when>
+      <when value="all">
+          <!-- do nothing -->
+      </when>
+    </conditional>
+  </inputs>
+  <outputs>
+  <data format="interval" name="out_file1" />
+  </outputs>
+  <tests>
+    <test>
+      <param name="input1" value="vcf2pgSnp_input.vcf" ftype="vcf" />
+      <param name="how" value="all" />
+      <output name="output" file="vcf2pgSnp_output.pgSnp" />
+    </test>
+  </tests>
+
+  <help>
+**Dataset formats**
+
+The input dataset is VCF_ format.
+The output dataset is pgSnp_.  (`Dataset missing?`_)
+
+.. _Dataset missing?: ./static/formatHelp.html
+.. _VCF: ./static/formatHelp.html#vcf
+.. _pgSnp: ./static/formatHelp.html#pgSnp
+
+-----
+
+**What it does**
+
+This converts a VCF dataset to pgSnp with the frequency counts being
+chromosome counts.  If there is more than one column of SNP data it will either
+accumulate all columns as a population or convert the column indicated
+to pgSnp.
+
+-----
+
+**Examples**
+
+- input::
+
+   1       13327   rs144762171     G       C       100     PASS    VT=SNP;SNPSOURCE=LOWCOV     GT:DS:GL        0|0:0.000:-0.03,-1.11,-5.00     0|1:1.000:-1.97,-0.01,-2.51     0|0:0.050:-0.01,-1.69,-5.00     0|0:0.100:-0.48,-0.48,-0.48
+   1       13980   rs151276478     T       C       100     PASS    VT=SNP;SNPSOURCE=LOWCOV     GT:DS:GL        0|0:0.100:-0.48,-0.48,-0.48     0|1:0.950:-0.48,-0.48,-0.48     0|0:0.050:-0.48,-0.48,-0.48     0|0:0.050:-0.48,-0.48,-0.48
+   1       30923   rs140337953     G       T       100     PASS    VT=SNP;SNPSOURCE=LOWCOV     GT:DS:GL        1|1:1.950:-5.00,-0.61,-0.12     0|0:0.450:-0.10,-0.69,-2.81     0|0:0.450:-0.11,-0.64,-3.49     1|1:1.500:-0.48,-0.48,-0.48
+   etc.
+
+- output as a population::
+
+   chr1    13326   13327   G/C     2       7,1     0,0
+   chr1    13979   13980   T/C     2       7,1     0,0
+   chr1    30922   30923   G/T     2       4,4     0,0
+   etc.
+
+- output for each column separately::
+
+   chr1    13326   13327   G       1       2       0       G/C     2       1,1     0,0     G       1       2       0       G       1       2       0
+   chr1    13979   13980   T       1       2       0       T/C     2       1,1     0,0     T       1       2       0       T       1       2       0
+   chr1    30922   30923   T       1       2       0       G       1       2       0       G       1       2       0       T       1       2       0
+   etc.
+
+</help>
+</tool>