Merge VCF INFO tags
Dear all,
I have a VCF file that, after annotation from VEP and extraction of tags with bcftools +split-vep ends up like:
[...]|amr|4.05357e-01||0|-0.143||||||;gnomADg_AF=0.341347,0.341347;[...]
Is there any way to merge the gnomADg_AF tag?
For example, choose the MIN() or MAX(), so that it ends up with a single number on that tag:
[...]|amr|4.05357e-01||0|-0.143||||||;gnomADg_AF=0.341347;[...]
thanks,
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My recommendation would be to do this in R or Python. VCFs are tabular, so you can easily manipulate the INFO field with
strsplit(..., split = "|")or.split('|'), then apply whatever logic you want for the gnomAD annotation.