Stop letting the shell interpret things on system()
Updates a call to system
Lowers QC priority, raises reduce reads RAM
Reserve some more RAM ahead of time for the reducing
really lower the priority
Up JAVA mem limits, stupid java
Adjusts threading/core/slots
Drops some priority, Changes some mem & thread/slot reservations
Updates bwa to 0.7.6a, updates GATK to 2.8-1-g932cd3a
Bumps the version number
Trims .list part from default output file name
caller opts instead of glm, Adds minPruning 3 for Haplo
Increase mem requests
Increases memory requests/reserves, always with the RAM
Disable fastqc, for awhile
Changes to use gatk 3.0, even though they say to use HaplotypeCaller now
Updates to GATK 3.0- no longer reduce reads or UnifiedGenotyper, gVCF HaplotypeCaller now
A few more small tweaks to RAM/Cores requested needed for various stages
Add check for tranches.pdf file, as the indels do not make it
Fixes tabix creation bug