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

Mutect2 --ignore-soft-clip-bases


We are running Mutect2 with the option to ignore soft clipped bases. This has significantly reduced our false positives, but the ALT and REF counts from the remaining reads do not seem to reflect what we see in IGV. Moreover, this seems to occur adjacent to the softclipped boundary. Could the softclipping index be off by 1?

Here's counts of alt and ref for one of these variants that we found:

                               ALT   REF    IGV-ALT   IGV-REF
          use softcipped       35    239     39       242
          ignore softclipped   37    235     4        237


Sign In or Register to comment.