Added parallizing options for various GATK tools. Fixed paths for test
for VCF steps where annot files have incompatible segment names
for dbsnp annotation file cleanup
Merge pull request #2 from ifx/master

Make file cleanup
Merge pull request #3 from ifx/master

Moved DATA_THREADS and CPU_THREADS into config.mk
commenting vqsr step for partial data run
temp for single chrom, merged config file and threading changes
first target is all
clean target
iterate all chroms
corner case for only one RG input file
script for metrics
make metrics also
merge
merge
use bash and not sh
use chromosomes var