Calculate the genotype frequency

Question

[SOHAIL]

Hi everyone:

I have a VCF file having multiple population samples. Is there any way to calculate the observed counts of genotypes called and observed genotype frequency of a subset of individuals from a given population within VCF file?

For example (genotype freq) : 0|0 : 0.2, 0|1: 0.5, 1|1: 0.3

just an analogous to --freq option in VCFtools field that calculates the allele frequency of REF and ALT allelic forms at given site.

Thanks a lot!

Regards, sohail.

Answer 1

[Wietje]

You might want to try PLINK which allows you to read in a VCF file (--vcf [INPUTFILE]), select only a few individuals (--keep [FILE]) and then get genotype frequencies with --freqx (with aditional option --nonfounders if you want to have it for all individuals in your list) or allele frequencis with --freq. Check the manual for more detailed information:

PLINK 1.9: https://www.cog-genomics.org/plink/1.9/

PLINK 2.0: https://www.cog-genomics.org/plink/2.0/

I hope this is of some help to you!