Question: Filtering using BED file
0
gravatar for errityf
2.4 years ago by
errityf0
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 • 1.1k views
ADD COMMENTlink modified 2.4 years ago by Devon Ryan1.9k • written 2.4 years ago by errityf0
0
gravatar for Devon Ryan
2.4 years ago by
Devon Ryan1.9k
Germany
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 2.4 years ago by Devon Ryan1.9k
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