SEQanswers (
-   Bioinformatics (
-   -   Filter VCF using external Allele Frequency (

rdoan 09-30-2014 04:19 AM

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?


Zaag 10-01-2014 01:08 AM

All times are GMT -8. The time now is 08:00 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.