Hi, I'm using GATK22.214.171.124 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.)