Genotype frequency from ped or vcf files

Question

[Ale Lope]

Hello All,

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!

Thanks,

Ale

Answer 1

[chrchang523]

plink2 --vcf <vcf filename> --geno-counts <column set modifier>

provides counts instead of 0..1 frequencies, but otherwise can report this information in a bunch of ways (see https://www.cog-genomics.org/plink/2.0/formats#gcount for the possible output columns, and https://www.cog-genomics.org/plink/2.0/general_usage#colset for column-set syntax).