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!