Question: Combining bed files from targeted sequencing panels using Bedtools intersect
gravatar for sdunbarr01
13 days ago by
sdunbarr0110 wrote:


I have 2 targeted sequencing panels, 1 is an exome and the other is an oncology panel and I combine them for capture and sequencing.

The panels share some of the same targets so I attempted to run a bedtools intersect to generate a single bed file for my analysis.

bedtools intersect -a exome.targets.bed.gz -b oncopanel.targets.bed.gz -v > ExomeOnly.bed

I am getting a really low on target rate and I suspect its something to do with my intersect.

what am I doing wrong?


next-gen forum bedtools • 72 views
ADD COMMENTlink modified 13 days ago by zx87549.9k • written 13 days ago by sdunbarr0110

why this option -v ?

ADD REPLYlink written 13 days ago by Pierre Lindenbaum134k

Questions like this are very open-ended and hard to answer. We do not see your data, only a command that will give the overlapping ranges between two files. Impossible to say anything here. The command is correct to get overlapping intervals between A and B. Not more to say at this point. For a better answer you would need to show some data, or anything that allows reproduction of what you see.

ADD REPLYlink written 13 days ago by ATpoint45k
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