Re: [Vcftools-help] vcf-annotate example annotates wrong column

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The command line suggests that you are running the latest packaged
version 0.1.4a, not the latest SVN version. I recommend using the SVN
code instead as it contains many new features and bug fixes.

Best,
Petr

On Wed, 2011-04-06 at 16:57 -0400, Powell, Eric wrote:
> That's strange.  I have the latest version.  I will keep trying to see if I can figure out what is happening.
> 
> -----Original Message-----
> From: Petr Danecek [mailto:pd...@sa...] 
> Sent: Wednesday, April 06, 2011 5:58 AM
> To: Powell, Eric
> Cc: 'vcf...@li...'
> Subject: Re: [Vcftools-help] vcf-annotate example annotates wrong column
> 
> 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
> > 
> > 
> > ------------------------------------------------------------------------------
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> 
> 
> 

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