I want to collect some metrics for my NGS panel.
To evaluate the capture efficiency of the probes, I want to calculate the on target rate from reads and base.
For reads, bedtools is applied to get the rate, however, reads can be calculate twice if they span two probes. Any method to avoid this?
To calculate the rate from base, I first get the depth file from bam using samtools. The sum of all these depth is listed as M. Then probe base depth was extracted from the depth file among those targets., which is listed as N. Base on target rate is calculated as N/M. Any quick guide for more efficient tool?