GATK4 MappingQualityReadFilter

Question

[jhy]

Hi, I'm using GATK4.1.5.0 Mutect2 for variant discovery.

This is my pre-processing step. Mapping, MergeBamAlignment, sorting, SetNmAndUqTags, MarkDuplicates, indexing, BaseRecalibrator, GatherBQSRReports, ApplyBQSR

I want to add "MappingQualityReadFilter" to the pre-processing step, can you tell me where to add it?

(I know there is a mapping quality filtering process in Mutect2, but I want to add it for other analyses such as CNV and structrual variation.)

Thanks.