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MuTect2 --filter_reads_with_N_cigar VS SplitNCigarReads

mattqdeanmattqdean CAMember
edited February 2016 in Ask the GATK team

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.

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by Sheila

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  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi Matt,

    You'd lose all reads spanning splice junctions from your analysis, which would probably dramatically lower your power to discover mutations in a lot of places. I wouldn't recommend doing this.

    No idea about TopHat behavior, sorry.

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