The Frontline Support team will be slow to respond December 17-18 due to an institute-wide retreat and offline December 22- January 1, while the institute is closed. Thank you for your patience during these next few weeks. Happy Holidays!
Release Notes can be found here.
How can I find the version of MuTect2 in broadinstitute_cga/MutationCalling_Mutect_v1-2_BETA_cfg?
I see for broadinstitute_cga/MutationCalling_Mutect_v1-2_BETA_cfg (described here) that MuTect1 uses the v1.1.6 jar but MuTect2 uses
/usr/local/bin/GenomeAnalysisTK.jar. Is there a way I can find out what version of GATK MuTect2 this configuration uses without running the workflow? I want to confirm I'm using the version of the jar that recently incorporated the strand bias filter. Thanks.