Bug Bulletin: we have identified a bug that affects indexing when producing gzipped VCFs. This will be fixed in the upcoming 3.2 release; in the meantime you need to reindex gzipped VCFs using Tabix.

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

loranialorania Posts: 9Member
edited September 2012 in Ask the team

Hi, 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,

Ania

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Comments

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 5,235Administrator, GSA Member admin

    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?

    Geraldine Van der Auwera, PhD

  • loranialorania Posts: 9Member

    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 Posts: 5,235Administrator, GSA Member admin

    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.

    Geraldine Van der Auwera, PhD

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