[Vcftools-help] vcf-validator INFO field errors

[Janet C. <ja...@pa...>]

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?