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Are there Quality score considerations for MinION data?

aminardsaminards Columbus, OhioMember

I am considering using the GATK to find variants in MinION data. I understand that the quality score values for MinION data are not standard scores. What considerations do I need to account for in the GATK pipeline when looking for variants?


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi @aminards,

    We've never looked at MINION data so we have no way to know, to be honest. The only thing I can say is that our tools place a lot of importance on base quality scores; it's possible to assign flat quality scores to all bases but that severely limits the caller's ability to weigh the evidence appropriately.

    Good luck and let us know how it goes.

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