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-   -   Filter VCF using external Allele Frequency (http://seqanswers.com/forums/showthread.php?t=47057)

rdoan 09-30-2014 04:19 AM

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

Zaag 10-01-2014 01:08 AM

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


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