Hi everyone,

I am working with the 1000 Genomes VCFs from the New York Genome Center (30x on GRCh38). The VCF obviously provides overall and superpopulation-specific alternative allele frequency. A small proportion of alternative allele frequencies are not the minor allele with values such as 0.8/0.9.

For example when I print %CHROM %POS %INFO/AF_EUR I can see this SNP, where the alternative allele frequency is clearly the major allele. (The VCF has already been filtered to keep just biallelic SNPs).

chr21 5245455 0.950237

I need to calculate and then filter on European superpopulation minor allele frequency. As the VCF comes, there is a key within INFO/AF_EUR. For all values in this column above 0.5 (indicating that the alternative allele is not the minor allele), I need to minus the value from 1 and create a new information field for European minor allele frequency. I have no idea how to go about manipulating this within a VCF, any tips? Thank you.