I recently received a batch of data from a targeted sequencing (50 genes, human) experiment. The sequencing was targeted on all exons of these 50 genes. I was suggested to calculate the minimum coverage for each exon, in case the coverage for the reads is not uniform.
As I'm still inexperienced, I was wondering how to calculate this. My idea would be, given that I have a BED file with the sequenced regions:
- Calculate per-base coverage for each BAM file using bedtools coverage and the BED file for the regions;
- Group the result by exon coordinate, and choose the minimum value for each coordinate.
Is there a better way, or is my approach totally off? Thanks!
In fact I'm using bedtools coverage to get the fraction of exons covered. I was wondering if there was anything else I could do.