Percentage of on target reads in custom capture sequencing
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.
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Pierre Lindenbaum
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ccagg
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ccagg
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# 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
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