Annotating a VCF [FORMAT not INFO field]

Question

[kate.ignatius]

Hi,

I'm annotating a vcf and have done this successfully in the past but I'm curious whether I can add a custom annotation in the FORMAT field rather than the INFO field.

cat file.vcf | vcf-annotate -a annotation.gz -d key=FORMAT,ID=anno,Number=.,Type=String,Description='custom annotation'  -c CHROM,FROM,TO,FORMAT/anno >  new.vcf

That is, where the GT:PL:GL information is usually.

Or can't this be done? The above code does not work. Though does work when you swap FORMAT with INFO.

Thanks!

[Cyriac Kandoth]

The FORMAT field describes the tags for each value in each genotype column. If your annotation file is going to add more tags, how are you assigning values per sample in the genotype columns? So whatever you're trying to do, can't be done with vcf-annotate. You're most likely going to need vcf-merge. Can you describe your overall goal, so we can help troubleshoot?