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

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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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