How to get allele frequency histogram from vcf file?

Jfly7 · 12-15-2014, 06:54 PM

Hi Everyone,

I am new to SEQanswers and the bioinformatics world, and I am looking for some help. I would like to get a count of allele frequencies in bins from a VCF file (i.e. to create a histogram).
For example, I would like a count of the number of alleles with frequency between 0-0.022, 0.022-0.1, 0.1-0.2, etc.
vcftools outputs the frequencies of each allele at each site, but I would like this summarized by counts within each frequency bin. I am wondering if any of you know of an easy way to do this?

Thanks!

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12-15-2014, 06:54 PM	#1
Jfly7 Junior Member Location: Montreal, Canada Join Date: Nov 2014 Posts: 4	How to get allele frequency histogram from vcf file? Hi Everyone, I am new to SEQanswers and the bioinformatics world, and I am looking for some help. I would like to get a count of allele frequencies in bins from a VCF file (i.e. to create a histogram). For example, I would like a count of the number of alleles with frequency between 0-0.022, 0.022-0.1, 0.1-0.2, etc. vcftools outputs the frequencies of each allele at each site, but I would like this summarized by counts within each frequency bin. I am wondering if any of you know of an easy way to do this? Thanks!