GATK.v3-1
Code cleanup in ReadPlinkPedigree
Fixed input parameter for GenotypeVCFs
Merge branch 'feature/GATK.v3.1' into develop
GATKv3.1, intersectCollect.pl, qcCollect.pl

- Added researchEthicalApproval tag for display in Scout
- Uppdated GATK to version 3.1
	- Removed HaplotypeCallerCombined
	- Removed ReduceReads
	- Added GenotypeVCFs
	- Added flag GATKGenoTypeGVCFsRefGVCFInfile
- Added IntervalTrees to intersectCollect.pl range queries
- Changed hash structure for exact queries intersectCollect.pl
	- run time speed up
	- allowing any number of keys (theoretically)
- Added slice queries for tabix files
- Code clean-up intersectCollect.pl
- minor changes qcCollect.pl
Annovar, RemoveRedundantFiles

- Added numerical sort after convert2annovar since in some cases oufile becomes unsorted
- Added tracking of "MostComplete" file to RemoveRedundantFiles
Minor changes
Added modules to RemoveRedundantFiles