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ReduceReads error: "Trying to clip before the start or after the end of a read"

loranialorania Member
edited September 2012 in Ask the GATK team

I'm running GATK version 2.1-8 with reads mapped to mm10. ReduceReads fails somewhere on chr2 with above message. From previous posts I understood that this bug has appeared already? Could you please help me to fix it?
Thank you,




  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Hi Ania,

    That sounds like a different bug, but please try again with the latest version (2.1-9).

    If the bug still occurs: can you please check that your bam file is valid, and if so upload the segment of the file where the problem is occurring so we can test it?

  • Thank you so much Geraldine for your suggestion!
    I didn't validate my file at first - and as picard/previous steps of my GATK pipeline weren't complaining about anything, so I thought it is ok.
    It turned out that my .bam files still have some reads without mates (I thought that picard fixmates takes care of it). When I filtered them out, the file validates and ReduceReads works fine.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    I'm happy to help. You normally don't need to validate files at every step, but when you get an error like this, validation is a good first step to troubleshooting the problem.

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