We've moved!
This site is now read-only. You can find our new documentation site and support forum for posting questions here.
Be sure to read our welcome blog!

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


Sign In or Register to comment.