Percentage of on target reads in custom capture sequencing

Question

[ccagg]

I have mapped bam files from an experiment where we designed a custom capture panel. I have a bed file of the regions we were trying to capture, and I want to know what percent of our bam reads overlap the bed file. When I have done a similar analysis with exome data, I've used picard HSmetrics, but it doesn't seem exactly right for this use case. I was wondering if there was a simple way to assess this without using picard or GATK.

Answer 1

[Pierre Lindenbaum]

# total reads mapped
samtools view -q 1 -F 3840  -c in.bam

# total reads mapped in capture
samtools view  -q 1 -F 3840 -L "capture.bed" -c in.bam