We have exome sequenced samples. I am planning to get the statistics for these exome samples using qualimap bamqc.
Actually, the mean coverage (2.28X) seems to be very low and also the coverage for every chromosomes i.e. around 1.5-3X. Then only I realized that the tool should consider only the length of exome in every chromosome instead of the entire chromosome length.
Considering the below exon length for calculating coverage (729,599,759 bases/8,079,409 exon bases = 90X coverage). **Is my understanding correct?
How do I change the settings in qualimap (bamqc) to consider only the exome length in every chromosome instead of entire chromosome length?**
Chr Total-Bases Exon Bases
chr1 249250621 8079409
chr2 243199373 5781424
chr3 198022430 4706998