how to do BQSR on WES or other targeted sequencing?
I have this question because of the following statement from this article:
In addition, there are some processing steps, such as BQSR, that should be restricted to the capture targets in order to eliminate off-target sequencing data, which is uninformative and is a source of noise.
My understanding is that it says the bias in BQS is different between on and off targets, i.e. the recalibration models should be different between on and off target bases. If that's correct, seems to me there are two proper ways of doing BQSR in WES, neither of which is in the Broad Official WES pipeline.
1. Keep variants only in the targets, i.e. apply
-L targets.bed -ip 100 at both steps of BQSR.
2. Keep variants in both on- and off-targets.
-L targets.bed at both steps of BQSR
-XL targets.bed at both steps of BQSR
2.3 merge the two bam files from 2.1 and 2.2
Just wonder if anyone can comment?