Question: Filtering using BED file
gravatar for errityf
22 months ago by
errityf0 wrote:

I have generated mpileups and I wish to filter the desired variants using a BED file. I have done this in the mpileup tool but it then wont allow me to filter further using VarScan. Is there a tool that will allow me to select variants based on a BED file after I generate the mpileup? Thanks.

bed file vcf mpileup filtering • 677 views
ADD COMMENTlink modified 21 months ago by Devon Ryan1.9k • written 22 months ago by errityf0
gravatar for Devon Ryan
21 months ago by
Devon Ryan1.9k
Devon Ryan1.9k wrote:

Assuming you're using the VCF format, then you should be able to use the "intersect intervals" (aka, bedtools intersect) tool to do this.

ADD COMMENTlink written 21 months ago by Devon Ryan1.9k
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