calculating allele frequencies in a vcf

Question

[eric.londin]

Hi all,

I have a vcf file that looks like this (two lines here):

1    144135212       rs1553120241    G       A       .       .       .       AN:AC   8560:5387       8:8     256:224 336:288 32:24   170:117 32:24   18:13   20:15   344:296 288:248 9432:6100
1     144148243       rs2236566       G       T       .       .       .       AN:AC   5996:510        0:0     0:0     0:0     0:0     0:0     0:0     0:0     84:8    0:0     0:0     6080:518

This file has an aggregated allele counts in the genotype columns (AN:AC) for each population group. I am interested in adding in the allele frequency for each population, so it would be the AC/AN, and add that as a third attribute to the genotype columns. These are the only attributes in the files and no other information is present.

so a potential output would be something like this:

1     144135212       rs1553120241    G       A       .       .       .       AN:AC:AF   8560:5387:0.629       8:8:1     256:224:0.875 336:288:0.857 32:24:0.75   170:117:0.68 32:24:0.75   18:13:0.722   20:15:0.75   344:296:0.86 288:248:0.861 9432:6100:0.646
1     144148243       rs2236566       G       T       .       .       .       AN:AC:AF   5996:510:0.085        0:0:0     0:0:0     0:0:0     0:0:0     0:0:0     0:0:0     0:0:0     84:8:0.95    0:0:0     0:0:0     6080:518:0.851

Does anyone know of a way to do this some easy fashion? I can't seem to figure out if a tool such as bcftools has the ability to do it. I can probably put together some script, but I wanted to see if there was something out there already that can do this.

Thanks for any help

Answer 1

[Kevin Blighe]

Hi, can you please try my solution, here: How to use bcftools to calculate AF INFO field from AC and AN in VCF?

Kevin