I'm looking to calculate some coverage statistics on the alignment in my targeted sequencing experiment. I have a BAM file and a BED file with the target regions. I wish to determine the percentage of bases covered above 30X, 40X, 50X etc. How can I best do this?
Also, we sequenced a LOT of samples in a single lane, so we had to repeat the experiment multiple times to get sufficient coverage. Will the above procedure help me determine if I have reached sufficient coverage? I wish to have at least 70X across the target region, but I can make do with a small percentage of low coverage regions.
I already have stats on average coverage per sample (by dividing number of bases sequenced on target by total length of target region)