Annotating a VCF ignoring ALT
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
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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.