Adding allele frequency to the genotype field of a VCF file

Question

[Nonny27]

I'm wondering if there is an way to get the allele frequency (AF1) from the INFO field VCF file into the genotype field instead (or as well), that way when I merge these files into a multi-sample VCF I can still easily access this information.

I have managed to isolate the allele frequency values from the INFO column using a sed command based on the flanking strings:

sed -e 's/.*;AF1=\(.*\);AN.*/\1/' file.vcf > output.txt

However, I can't work out how to append this to the genotype field. ie. GT:GQ:PL:AF1

Any help would be greatly appreciated!

Answer 1

[Zev.Kronenberg]

VCFFIXUP in vcflib should do what you want.

https://github.com/vcflib/vcflib