Bug fixes and working variantannotation

 Changes to be committed:
	modified:   GenerateScripts.sh
	modified:   parameters.csv
	modified:   protocols/AddOrReplaceReadGroups.sh
	modified:   protocols/CollectRnaSeqMetrics.sh
	modified:   protocols/GatkHaplotypeCaller.sh
	modified:   protocols/GatkSnpEffVariantAnnotation.sh
	modified:   protocols/GatkSplitAndTrim.sh
	modified:   protocols/MarkDuplicates.sh
	modified:   protocols/StarRunAlignmentP1.sh
	modified:   protocols/StarRunAlignmentP2.sh