Calculate minor allele frequency from VCF

Question

[rshoobs]

Hi All!

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

Where
RefPanelAF="Allele frequency in imputation reference panel"
AC="Allele count in genotypes
AN="Total number of alleles in called genotypes

Answer 1

[Pierre Lindenbaum]

see How to use bcftools to calculate AF INFO field from AC and AN in VCF?

[rshoobs]

yes this is perfect! has a MAF option I can use