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Published 20 hours ago • verified publisher icon broadinstitute

GatherBamFiles Indexing Bug

Open gudeqing opened this issue 5 years ago • 8 comments

Hi, I am testing GatherBamFiles of gatk-4.1.4.1 and gatk-4.1.2.0: when I set '--CREATE_INDEX false', the command goes well and the resulted bam could be indexed by samtools, however, when I set '--CREATE_INDEX true', exception printed, such as "Exception in thread "BamIndexingThread" htsjdk.samtools.SAMException: Exception creating BAM index for record A00234:397:HTKTWDSXX:1:1266:22453:5807 2/2 135b aligned to chrM:1-131.". Thus, I think this could be a bug. By the way, BuildBamIndex also fails to build index for the resulted bam. With Regards!

gudeqing avatar Jan 17 '20 02:01 gudeqing