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
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
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