Question: Calculate minor allele frequency from VCF
gravatar for rshoobs
2.2 years ago by
rshoobs10 wrote:

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

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

snp genome • 4.1k views
ADD COMMENTlink modified 2.2 years ago • written 2.2 years ago by rshoobs10
gravatar for Pierre Lindenbaum
2.2 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum133k wrote:

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

ADD COMMENTlink written 2.2 years ago by Pierre Lindenbaum133k

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

ADD REPLYlink written 2.2 years ago by rshoobs10
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