Changed MarkDuplicates to MarkDuplicatesWithCigar, Added USE_THREADS to MergeSam
Node processing efficieny
- More aggresive scatter/gather
- Internal processing queue at node
- Contigs size ordered
- Prcessed GenoTypeGVCFs as seperate contigs on each node
- Annotation via piping to SnpEff and vcfParser
- Removed Sort module and added it as mandatory after alignment
- Added Chanjo version to qcmetrics via qccollect