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?