Question: Combining bed files from targeted sequencing panels using Bedtools intersect
1
gravatar for sdunbarr01
13 days ago by
sdunbarr0110
sdunbarr0110 wrote:

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!

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
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1646 users visited in the last hour
_