Filter VCF using external Allele Frequency

rdoan · 09-30-2014, 05:19 AM

Hello,
I would like to filter large multi-sample VCFs using allele frequencies obtained from VCFs or tab files from the EVS and 1000G datasets.

I know that GATK and VCFtools can filter for allele freqs within a VCF, but they don't seem to offer a method to remove variants with a set frequency from an external source such as EVS or 1000G.

Is there a tool/command to do this without having to create a list of variants from the databases and specifically remove them?

Thanks

Zaag · 10-01-2014, 02:08 AM

http://statgenpro.psychiatry.hku.hk/...q/download.php

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09-30-2014, 05:19 AM	#1
rdoan Member Location: USA Join Date: Oct 2012 Posts: 10	Filter VCF using external Allele Frequency Hello, I would like to filter large multi-sample VCFs using allele frequencies obtained from VCFs or tab files from the EVS and 1000G datasets. I know that GATK and VCFtools can filter for allele freqs within a VCF, but they don't seem to offer a method to remove variants with a set frequency from an external source such as EVS or 1000G. Is there a tool/command to do this without having to create a list of variants from the databases and specifically remove them? Thanks

10-01-2014, 02:08 AM	#2
Zaag Senior Member Location: Amsterdam Join Date: Nov 2009 Posts: 112	http://statgenpro.psychiatry.hku.hk/...q/download.php