does bcftools has anything like vcf-check?

Question

[roalva1]

Hello,

I am merging 14k vcfs and I get this error:

[W::vcf_parse] INFO 'D' is not defined in the header, assuming Type=String
Error: The INFO field is not defined in the header: D

So, I think I have some vcf that is not well formatted for bcftools, would you know if bcftools has something like vcf-check? I haven't seen it. Then, I could remove this vcf.

Thanks

[roalva1]

I've just discovered a truncated file. Sorry!!!!

Answer 1

[Pierre Lindenbaum]

here is a command to find the VCF missing the INFO/D in the header

$ find dir -name "*.vcf.gz" | while read F; do gunzip -c "$F" | grep "^##INFO=<ID=D," > /dev/null || echo $F ; done

[roalva1]

I think there is a problem with bcftools, becuase I do this:

zgrep   ";D=" ./*.vcf.gz > D.txt

and I get an empty file