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From: Janet C. <ja...@pa...> - 2017-09-08 17:46:40
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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? |