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

Member Posts: 9
edited September 2012

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

Tagged:

Hi Ania,

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

• Member Posts: 9

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.