Re: [Vcftools-help] vcf-validator INFO field errors

[Petr D. <pd...@sa...>]

Thank you Janet. Just pushed a fix which should resolve the problem,
please try with the latest Vcf.pm
https://github.com/vcftools/vcftools

Best wishes,
Petr

On Fri, 2017-09-08 at 17:03 -0400, Janet Cady wrote:
> Sure. Here's a small vcf file I generated and the results I got when
> I ran vcf-validator.
> Thanks!
> 
> Janet
> 
> > 
> > On Sep 8, 2017, at 3:52 PM, Petr Danecek <pd...@sa...> wrote:
> > 
> > Hi Janet,
> > 
> > that is curious. Any chance you could share a small test case to
> > reproduce the behavior? 
> > 
> > Best wishes,
> > Petr
> > 
> > 
> > On Fri, 2017-09-08 at 13:30 -0400, Janet Cady wrote:
> > > 
> > > I generated a VCF file using the command:
> > > 
> > > 	samtools mpileup -f ref.fa -uv sample.bam -t
> > > INFO/AD,INFO/ADF,INFO/ADR | bcftools call -m -A -o sample.vcf
> > > 
> > > 
> > > When I run vcf-validator on the resulting file I get a message
> > > like
> > > this for all positions with no ALT alleles:
> > > 
> > > 	INFO field at chrM:16567 .. INFO tag [AD=154] expected
> > > different number of values (expected -1, found 1),INFO tag
> > > [ADF=151]
> > > expected different number of values (expected -1, found 1),INFO
> > > tag
> > > [ADR=3] expected different number of values (expected -1, found
> > > 1)
> > > 
> > > Positions with one or more ALT alleles don't get have any
> > > messages.
> > > 
> > > The meta-information lines for these fields say:
> > > 	##INFO=<ID=AD,Number=R,Type=Integer,Description="Total allelic
> > > depths">
> > > 	##INFO=<ID=ADF,Number=R,Type=Integer,Description="Total allelic
> > > depths on the forward strand">
> > > 	##INFO=<ID=ADR,Number=R,Type=Integer,Description="Total allelic
> > > depths on the reverse strand">
> > > 
> > > Based on the VCF spec (v4.2), Number=R means that these fields
> > > should
> > > have a value for each possible allele including the reference.
> > > Doesn't this mean it should have 1 value? Why would it expect -1
> > > values?
> > > 
> > > 
> > > 
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> > 
> > -- 
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> > Limited, a charity registered in England with number 1021457 and a 
> > company registered in England with number 2742969, whose
> > registered 
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> > 
> 


-- 
 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.