I would like to get the genotype frequency at each SNP for a specific cohort. I have 2,000 patients divided into three different diseases, so I would like to reproduce the next output (as an example) per each cohort:
AA AT TT CC CG GG SNP1 .6 .3 .1 - - - SNP2 - - - .2 .5 .3 SNP3 - - - .4 .4 .2 : SNPN .6 .3 .1 - - -
I have .ped and vcf files format
Hopefully someone can give me a hint!