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GATK Clipreads bug

dr153dr153 DukeMember

Hi there,
It looks like the latest version of GATK has a bug when you softclip adapters and change clipped reads to N and quality scores to zero (WRITE_NS_Q0S) , this option results in malformed SAM/BAMS
This used to work fine in previous versions

Issue · Github
by Sheila

Issue Number
Last Updated


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