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Does MuTect 1.1.4 properly handle reads aligned with bwa mem, with or without '-M'?

kw10kw10 CambridgeMember

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.



  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    If the supplementary alignments are not marked as such, MuTect will have no way to know that it should not use them.

  • kw10kw10 CambridgeMember

    Hi Geraldine,

    With bwa mem, there are supplementary reads, flagged with 0x800, and secondary reads, flagged with 0x0100. The 0x800 flag is new in bwa mem - bwa aln did not use this flag. So, I was wondering if MuTect has also been updated to process (ignore?) reads with flag 0x800 and treat them as they would reads that have a flag 0x0100.


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Ah, thanks for clarifying, and sorry for the much delayed response. That would be handled internally by the htsjdk library, which treats supplemental alignments the same way as secondary alignments in the SAMRecord code as far as I can tell. So it depends whether the SAMRecord was already handling this flag in the version that was included in GATK and MuTect at the time it was built (~June 2013). I believe that is the case but can't guarantee it. My expectation is that if you run MuTect on your data aligned with BWA-MEM, it will either run smoothly if the flags are handled, or blow up if not.

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