Merge VCF INFO tags

Question

[FGV]

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,

[Brice Sarver]

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.