Question: Difference in .bed target region base count and mapped base count for different tools
gravatar for gavehan
4 months ago by
gavehan0 wrote:


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!

tool samtools gatk software • 126 views
ADD COMMENTlink written 4 months ago by gavehan0
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