Fixes it to use better working dir & input/output paths
Ups memory limits & drops some threads for better HUGE project running
Another script
Lowers BAM compression a bit, we are spending a little too much CPU time for little storage compression
Ups to use gatk 2.5-2-gf57256b
Ups mem for reduce reads, I'm tired of the WGS failing due to lack of the ram
Fixes memory request & removes extra $
Adds in initial new bwa mem wrapper
Changes bwa mem to pipe to picard for sort right away
Changes to use new bwa_mem which takes fastq directly & outputs sorted bam/sam