Difference in .bed target region base count and mapped base count for different tools

Question

[gavehan]

Hello!

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!

Answer 1

[Pablo Marin-Garcia]

One of the main differences between coverage software are the default they use. You need to read about the defaults used in each software and version (sometimes it change over time).

Things to look at:

• do they count the duplicated reads?
• do they filter by mapping quality?. Some filter mapq = 0
• do they filter by read length?
• do they skip the deletions from the CIGAR line?
• if you are doing a coverage by region, how is the coverage summarized? All the reads? only the ones full enclosed in the region? The ones with partial overlap need x% of overlapping?...... ....

The specific answer would depend of your commands and software versions