Hello,
I have a pipeline to do variant calling and a some point there is the GATK FilterMutectCalls
tool which annotate the variants, and some get flagged "map_qual" when the mapping quality is low. By default, I remove them from the variant calling results. But for some variants I noticed there is a very high number of reads with good alignment quality, they "looks" good on IGV. So my question is:
What is the risk of keeping those variants in my variant calls? I'm not sure I understand well what does mapping quality represents.