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Old 09-30-2014, 04:19 AM   #1
Location: USA

Join Date: Oct 2012
Posts: 10
Default Filter VCF using external Allele Frequency

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?

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