what does it mean to cap mapping quality of poorly mapped reads
Entering edit mode
13 months ago
Repo1 • 0

Hello guys,

I was following a tutorial proposed by galaxy server which you can find here

In this tutorial we want to identifIy germline and somatic variants from normal and tumor data. Reads were mapped using the BWA-MEM tool.

When I got to the mapped reads preprocessing and in the read mapping qualities recalibration step specifically I came across this option that says "Coefficient to cap mapping quality of poorly mapped reads" and it was set to 50. the tutorial says "It is an empirical, but well-established finding that the mapping quality of reads mapped with bwa should be capped this way before variant calling."

So I wanted to know what do they mean by capping mapping quality?

BWA-MEM bam variant-calling • 259 views

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