Summarise genotypes in a VCF file

Question

[Dave Tang]

Dear all,

I have created a multi-sample VCF file from HapMap data that only contains genotypes (GT). I am looking for a program/tool that can calculate the allele frequencies (AF) and allele counts (AN), and have them subsequently added to the INFO field. It's not that difficult to script up, but I was wondering if a tool already exists to do this.

Thanks!

Dave

Answer 1

[Dave Tang]

Use vcflib available at https://github.com/vcflib/vcflib and the vcffixup tool.

cat output.vcf | grep -v "^#" | head -1
chr21   9889293 rs28676788 G    A       .       .       .       GT      0/0     ./.     0/0     0/0     0/0     0/0     0/0     0/0     0/0     1/0     0/0     1/0     1/0     0/0     0/0     0/0     0/0     0/0     0/0     0/0     0/0     0/0     0/0     0/0     0/0    0/0      0/0     0/0     0/0     0/0     0/0     0/0     0/0     0/0     1/0     1/0     1/0     0/0     0/0     0/0     0/0     0/0     0/0     1/0     0/0     0/0     0/0     0/0     0/0     0/0     ./.     0/0     0/0     0/0     0/0     1/0     1/0     0/0     0/0    ./.      0/0     0/0     ./.     1/0     0/0     0/0     0/0     0/0     0/0     0/0     0/0     0/0     1/0     0/0     0/0     0/0     1/0     1/0     1/0     0/0     0/0     1/0     1/0

vcffixup output.vcf | grep -v "^#" | head -1
chr21   9889293 rs28676788 G    A       0       .       AC=16;AF=0.101266;AN=158;NS=83  GT      0/0     ./.     0/0     0/0     0/0     0/0     0/0     0/0     0/0     1/0     0/0     1/0     1/0     0/0     0/0     0/0     0/0     0/0     0/0     0/0     0/0     0/0    0/0      0/0     0/0     0/0     0/0     0/0     0/0     0/0     0/0     0/0     0/0     0/0     1/0     1/0     1/0     0/0     0/0     0/0     0/0     0/0     0/0     1/0     0/0     0/0     0/0     0/0     0/0     0/0     ./.     0/0     0/0     0/0     0/0     1/0    1/0      0/0     0/0     ./.     0/0     0/0     ./.     1/0     0/0     0/0     0/0     0/0     0/0     0/0     0/0     0/0     1/0     0/0     0/0     0/0     1/0     1/0     1/0     0/0     0/0     1/0     1/0

NS refers to the number of calls, i.e. the number of samples. 4 samples had no genotype, i.e. ./., therefore AN is 79*2 = 158. AC is the alternate allele count and AF is the alternate allele frequency.