broadinstitute/gatk 4.0.1.2

on GitHub

This is a small bug fix release to fix issues in the WDLs for Mutect2 and the CNV tools. It also includes a newer version of the GKL (Genomics Kernel Library) with some compression-related performance improvements.

As usual, a docker image for this release can be downloaded from https://hub.docker.com/r/broadinstitute/gatk/

• Mutect2 WDL:
  • Handle sample names with spaces correctly (#4360)
  • Pass VCF indices correctly (#4381)
• CNV somatic pair workflow and somatic panel workflow WDLs:
  • Fixed mem_gb_for_model_segments parameter and exposed additional memory parameters (#4364)
• Update to GKL version 0.8.3 with compression-related performance improvements (#4311)