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How does MAPQ affect haplotypecaller during germline calling
I understand that, during germline calling, pairHMM calculates the likelihood of each haplotype by taking base quality into consideration.
My question is: what role does MAPQ play during germline calling?
For example in low mapperable region, we may get alignment with multiple mismatch within a short window or alignment of multiple hits. these situation of low MAPQ alignment should be considered by haplotypecaller, right? Can anyone share some insight on this?