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MuTect2 --filter_reads_with_N_cigar VS SplitNCigarReads
I am calling variants in RNA-seq data. From the guide posted here, I know that Split'N'Trim is part of the workflow which has ALLOW_N_CIGAR_READS.
I am wondering if I simply use Mutect2 --filter_reads_with_N, would I be losing out on anything during downstream analysis?
I do not have to reassign MQ to unique mappers as I have set it to 60 (instead of 255) in STAR. By chance, does TopHat2 preserve MQ of each read bases? Ideally I'd like to filter variants using MQ down the road.