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Calculate minor allele frequency from VCF

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

snp genome
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written by rshoobs • rshoobs

1 answer

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

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written by rshoobs • rshoobs

I've moved Pierre's comment to an answer. You can accept it to give this post closure.

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• 0 views • link
written by Ram Ram

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