Annotating a VCF ignoring ALT

Question

[loy_loy]

Hi everyone,

I want to annotate a VCF and I am using bcftools annotate. It works so far but I also want to annotate variants according only to their position. So I am searching for a function to ignore the ALT field. Is this possible with bcftools?

Thank you!

Best
Lynn

[raphael.B]

Hello, where does your annotation comes from? If you use a bed file (with no REF and ALT) columns, bcftools should do the matching according to the position of the variant only.