Combining bed files from targeted sequencing panels using Bedtools intersect

Question

[sdunbarr01]

Hello,

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?

Thanks!

[Pierre Lindenbaum]

why this option -v ?

[ATpoint]

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.