umake - fail on deprecated OUT_PREFIX
Cleanup align/umake output when no prameters specified
UMAKE - fix to not fail on empty VCFs
umake - update to use GOTCLOUD_ROOT in path to runcluster
SNPcall - add -k option to make
Thunder - set a default number of states
Thunder - set a default number of states - actual fix, previous version had the fix commented out
SnpCall - add option to have dependency on BAMs
Merge in latest from Master