I was initially doing performance comparison for tools to obtain sample wide average depth of coverage.
I compared several tools listed below
Qualimap, GATK - DepthOfCoverage, Mosdepth and Samtools - Bedcov
However, the tools return different numbers for
1. Target region base count (region of interest specified by a .bed file)
2. Mapped base count (from the .bam file)
I was wondering if anyone can inform me on why the numbers are different...
I know for a fact that 'Mapped base count' can differ due to the tools algorithm in counting the mapped reads / bases (pileup, events, window and etc...)
But I cannot find information regarding the difference for the 'Target region base count'
Thanks in advance for your help!