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SplitNCigarReads Unsupported Cigar Operator: =


I got this error when trying to run SplitNCigarReads on a BAM file. I checked the source that generates this exception, and it appears that (as may be expected from the name), there is no handling for some Cigar String Operators.

The BAM specification states that '=' is perfectly fine. So... what gives?

Issue · Github
by Sheila

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  • SheilaSheila Broad InstituteMember, Broadie ✭✭✭✭✭


    Can you please tell us the exact command you ran and the version you are using?


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    @cacampbell To specifically address your original question: you're correct that this tool does not handle the '=' operator, even though the spec allows for it. This is a limitation of the current incarnation of the tool due to an oversight at the time it was written -- we rarely encounter those operators in the data we see so we did not think to test for them . I believe the updated version that is going into GATK4 is not subject to that limitation, so feel free to give that a spin when it goes in if you'd like.

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