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Question: Filtering using BED file
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gravatar for errityf
2.4 years ago by
errityf • 0
errityf • 0 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
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modified 2.4 years ago by Devon Ryan • 1.9k • written 2.4 years ago by errityf • 0
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gravatar for Devon Ryan
2.4 years ago by
Devon Ryan • 1.9k
Germany
Devon Ryan • 1.9k 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 COMMENT • link written 2.4 years ago by Devon Ryan • 1.9k
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