I have a bed of my targets (start and stop coordinates of each exon of my genes of interest). I have a BAM file generated from my ION PGM run. I am trying to identify any location identified in my BED file where I have less than 20x coverage so I can fill in these regions with traditional Sanger sequencing.
Basically, if any bases within the exon are covered at less than 20x, I want to know which. (I have heard 20x is a good threshold for germline variants, agreed?)
Also, if I add a descriptive section to the BED file contain “gene-exon” that could be included would be even more helpful.
I have been reading post online for days, and I am lost here. Can anybody help please?