Philipp Hähnel

Hi @davidbenjamin , this ticket is already open for a while, but I haven't found a sensible multi-sample wdl yet, so I've spent some time putting a multi-sample calling workflow...

I cleaned up the mutect2 wdl and added multi-sample support. I also optimized resource usage and exposed the memory parameters: https://github.com/phylyc/gatk4-somatic-snvs-indels

Hi, regarding making --linked-de-bruijn-graph the default, I wanted to share that I had recently run mutect2 (gatkv4.2.6.1) on a larger cohort of samples with that option, some of which had...