Question: Calculate the genotype frequency
gravatar for SOHAIL
2.6 years ago by
Beijing Institute of Genomics, CAS.
SOHAIL320 wrote:

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.

ngs vcf • 1.7k views
ADD COMMENTlink modified 2.6 years ago by Wietje210 • written 2.6 years ago by SOHAIL320
gravatar for Wietje
2.6 years ago by
Wietje210 wrote:

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:

PLINK 2.0:

I hope this is of some help to you!

ADD COMMENTlink written 2.6 years ago by Wietje210
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