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Does MuTect 1.1.4 properly handle reads aligned with bwa mem, with or without '-M'?
I have BAMs aligned with bwa mem and the '-M' flag was not used, so supplementary read alignments are not marked as secondary. I am wondering if MuTect v1.1.4 will ignore these reads or if I should realign with bwa mem -M to mark these alignments as secondary.