I have sanger imputed genotype files and want to filter them based on MAF. Unfortunately they do not contain MAF scores. Is there an easy way to calculate MAF from this file? For reference here is an exmaple of what it does contain:
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT LD1_LD1 ... 10 61694 rs546443136 T G . PASS RefPanelAF=0.0288539;AN=154;AC=0;INFO=1.24993e-09 GT:ADS:DS:GP 0|0:0.05,0.05:0.1:0.9025,0.095,0.0025 10 75803 . T C . PASS RefPanelAF=0.672316;AN=154;AC=154;INFO=9.82505e-10 GT:ADS:DS:GP 1|1:0.65,0.65:1.3:0.1225,0.455,0.4225 10 77582 . A G . PASS RefPanelAF=0.471449;AN=154;AC=0;INFO=-3.76292e-09 GT:ADS:DS:GP 0|0:0.45,0.45:0.9:0.3025,0.495,0.2025
RefPanelAF="Allele frequency in imputation reference panel"
AC="Allele count in genotypes
AN="Total number of alleles in called genotypes