Hi - I am trying to use bcftools to overwrite the existing FMT/GT values in a VCF file, matching by the ID column, in addition to CHROM and POS.
I tried creating a .txt.gz file as an annotation file, but got a message that to update the FMT/GT values, I must use a VCF as my annotation file. I have done this, and then I am using:
bcftools1.18 annotate -a annotest.vcf.gz -c ~ID,FMT/GT -O z -o new.vcf.gz original.vcf.gz
When I do this, I get a note that says:
"todo: -c ~ID with -a VCF?"
Does this means that bcftools does not allow me to update FMT/GT using the ID column?
Thanks in advance!
•
written
by
karen2 •
1 answer
the message is here
https://github.com/samtools/bcftools/blob/develop/vcfannotate.c#L2236
where tgts_is_vcf is set here https://github.com/samtools/bcftools/blob/develop/vcfannotate.c#L3512 when the annotation format is a VCF
if ( type.format==vcf || type.format==bcf )
{
args->tgts_is_vcf = 1;
so the syntax using '~ID' only works with tabix indexed files, not VCF
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