To celebrate the release of GATK 4.0, we are giving away free credits for running the GATK4 Best Practices pipelines in FireCloud, our secure online analysis portal. It’s first come first serve, so sign up now to claim your free credits worth $250. Sponsored by Google Cloud. Learn more at https://software.broadinstitute.org/firecloud/documentation/freecredits

Usage of "--dontUseSoftClippedBases" HaplotypeCaller option for exom enrichment data

Hi GATK Team,
HaplotypeCaller does not call structural variants from soft clipped bases, therefore the "--dontUseSoftClippedBases" should mainly reduce false positives (e.g. incomplete adapter trimming)? Is this thought correct or am i wrong?

Greetings from Munich

Best Answer

Answers

Sign In or Register to comment.