I'd be grateful for some help please.
I've got several joint-called trio VCFs (unaffected parents and proband) which I'm analysing. The multi-sample vcf nicely shows 0/0, 0/1, 1/1 for each individual per variant. However, I'd like to convert the notation to three columns of simply het, hom and ref to make it much easier to analyse.
I've checked out the annovar script convert2annovar.pl --withzyg, however this only works for individual sample vcfs which isn't what I need. I'd like all the samples together in the same multi-sample vcf but with zygosity stated for each variant.
Any help or suggestions would be greatly appreciated. E