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From: Petr D. <pd...@sa...> - 2011-04-06 09:58:18
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Hi Eric, can you please try with the latest SVN version? I was not able to reproduce your error. svn checkout https://vcftools.svn.sourceforge.net/svnroot/vcftools vcftools Thanks, Petr On Tue, 2011-04-05 at 11:34 -0400, Powell, Eric wrote: > I am trying to replicate the vcf-annotate example. > > > > My command line is: > > ----------------------------------------------------------------------------- > > /mihg/users/epowell1/gatk/vcftools_0.1.4a/bin/vcf-annotate -a > annotate.txt.gz -c FROM,TO,CHROM,INFO/HM2,INFO/GN,INFO/DP -d > key=INFO,ID=HM2,Number=0,Type=Flag,Description=HapMap2 membership -d > key=INFO,ID=GN,Number=1,Type=String,Description=Gene Name -d > key=INFO,ID=DP,Number=0,Type=Integer,Description=Depth,etc /mihg/users/epowell1/gatk/vcftools_0.1.4a/examples/concat-a.vcf > > > > The format of annotate.txt.gz is: > > ----------------------------------------------------------------------------- > > [epowell1@mendel1 test_annotate_example]$ zcat annotate.txt.gz > > 100 100 1 HM2 gene1 5 > > 110 110 1 0 . 6 > > 130 130 1 HM2 . 7 > > 140 140 1 0 . 8 > > 150 150 1 0 . 9 > > 110 150 2 HM2 gene2 . > > 160 160 2 0 gene3 11 > > > > Unfortunately, while I do not get any errors, the output is not > correct: > > ----------------------------------------------------------------------------- > > [epowell1@dfa test_annotate_example]$ perl $vcfannotate -a $annot.gz > -c FROM,TO,CHROM,INFO/HM2,INFO/GN,INFO/DP -d > key=INFO,ID=HM2,Number=0,Type=Flag,Description="HapMap2 membership" > -d key=INFO,ID=GN,Number=1,Type=String,Description="Gene Name" -d > key=INFO,ID=DP,Number=0,Type=Integer,Description="Depth,etc" $invcf > > ##fileformat=VCFv4.0 > > ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth"> > > ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> > > ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> > > ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth"> > > ##FILTER=<ID=q10,Description="Quality below 10"> > > ##INFO=<ID=HM2,Number=0,Type=Flag,Description="HapMap2 membership"> > > ##INFO=<ID=GN,Number=1,Type=String,Description="Gene Name"> > > ##source_20110305.1=/mihg/users/epowell1/gatk/vcftools_0.1.4a/bin/vcf-annotate -a annotate.txt.gz -c FROM,TO,CHROM,INFO/HM2,INFO/GN,INFO/DP -d key=INFO,ID=HM2,Number=0,Type=Flag,Description=HapMap2 membership -d key=INFO,ID=GN,Number=1,Type=String,Description=Gene Name -d key=INFO,ID=DP,Number=0,Type=Integer,Description=Depth,etc /mihg/users/epowell1/gatk/vcftools_0.1.4a/examples/concat-a.vcf > > #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT > A > > ;GN=gene1;HM2 GT:GQ:DPGTTT 0/1:409:3506 q10 DP=5 > > 1 GT:GQ:DP. 0/1:245:32 1792 PASS DP=6 > > 1 120 . GA G 628 q10 DP=21 > GT:GQ:DP 1/1:21:21 > > ;HM2 GT:GQ:DP. 0/1:212:22 1016 PASS DP=7 > > 1 GT:GQ:DP. 0/1:150:30 727 PASS DP=8 > > 1 GT:GQ:DP. 1/2:12:10A,T 246 PASS DP=9 > > 1 160 . TAAAA TA,T 246 PASS DP=10 > GT:GQ:DP 1/2:12:10 > > 2 100 . GTTT G 1806 q10 DP=35 > GT:GQ:DP 0/1:409:35 > > ;GN=gene2;HM2 GT:GQ:DPCAAA 0/1:245:3292 PASS DP=. > > ;GN=gene2;HM2 GT:GQ:DPGA 1/1:21:2128 q10 DP=. > > ;GN=gene2;HM2 GT:GQ:DPGAA 0/1:212:2216 PASS DP=. > > ;GN=gene2;HM2 GT:GQ:DPGT 0/1:150:307 PASS DP=. > > ;GN=gene2;HM2 GT:GQ:DPTAAAA 1/2:12:1046 PASS DP=. > > ;GN=gene360 GT:GQ:DPTAAAA 1/2:12:1046 PASS DP=11 > > > ------------------------------------------------------------------------------ > Xperia(TM) PLAY > It's a major breakthrough. An authentic gaming > smartphone on the nation's most reliable network. > And it wants your games. > http://p.sf.net/sfu/verizon-sfdev > _______________________________________________ Vcftools-help mailing list Vcf...@li... https://lists.sourceforge.net/lists/listinfo/vcftools-help -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. |