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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?
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
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.
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.