Request to adjust GATK3's memory requirement for an individual job

[vinayakvsv]

I'm using this issue to make a feature request. In snakefile.gatk3_joint, the memory requirement is fixed at -Xmx3500M -Xms3500M. However, for some scan2 makepanel runs, the memory requirement for an individual variant calling job is not enough to complete the job, so the makepanel job doesn't go to completion. One solution might be to increase the requirement to 7000M, for example -Xmx7000M -Xms7000M. I had to manually modify snakefile.gatk3_joint, but is there a way to toggle this memory requirement in the job config file? Thanks.