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Should SplitNCigarReads still be run even though BWA was the aligner used?

We are working with 176 BAMs that were aligned using BWA and have just finished the AddOrReplaceReadGroupsstep of the RNAseq workflow. The next step, SplitNCigarReads, appears to assume that STAR aligner was used - is this still applicable to a BWA-aligned BAM or should we skip this step?


  • bshifawbshifaw Member, Broadie, Moderator admin
    edited April 2019

    SplitNCigarReads does two things:
    1. "splits reads into exon segments (getting rid of Ns but maintaining grouping information)" added by STAR aligner
    2. "hard-clip any sequences overhanging into the intronic regions." (Review this article for details, keep in mind it's a doc for GATK3)
    Since BWA will not add Ns to your CIGAR than you shouldn't have any trouble with related errors in the proceeding GATK tools. However, you may still have overhangs in your bam file, if you don't mind leaving them in then you could probably skip SplitNCigarReads.

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