tools to calculate Exac population specific frequency

Question

[jan]

HI,

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 ?

[poisonAlien]

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.

[gaelgarcia05]

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'.

[jan]

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..