Hi Jason,
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.