Question: tools to calculate Exac population specific frequency
gravatar for jan
3.7 years ago by
Sydney, Australia
jan130 wrote:


I have 500+ MAF files of exome sequencing. I want to get the allele frequency for all population in Exac.

I have used awk script to match my variants in MAF files with the VCFs from EXac database. However, Exac only provides the allele count and allele number (AC ; AN) for population specific and I need to calculate the frequency.

Is there a tool or script available to calculate the population specific allele frequency from Exac database ?

sequencing exac maf • 1.8k views
ADD COMMENTlink written 3.7 years ago by jan130

Variant Effect Predictor has ExAC plugin which will annotate your variants with ExAC population wise Allele Frequencies. If you're willing to spend some time, re-annotate youre MAF files using scripts like vcf2maf/maf2maf, which wraps around VEP and also does transcript prioritization.

ADD REPLYlink written 3.7 years ago by poisonAlien2.8k

Hi Jan,

Wondering if you ended up finding an effective way to do this? I'm currently trying to do the same thing — except I don't relally understand what you mean by 'MAF files'.

ADD REPLYlink written 2.3 years ago by gaelgarcia05210

I ended up following above suggestion. MAF (mutation allele format) is a format of my variant file. My sequencing vcf files were initially anonated with snpEff and in-house qSNP.

So what we did was to re-annotate vcf files using VEP and use their ExAC plugin which can calculate frequency from AN, and AF..

ADD REPLYlink written 2.3 years ago by jan130
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