Initial checkout, workflow is not working yet
Added samtools
fixed symbolic file link problem
realignerTargetCreator seems to work
Separated the .fai, .dict and .bai creation step
Runs up to BaseRecalibrator
Deleted deft ask ReduceReads, this worker is no longer supported with GATK 3.0
Gets to the point where a VCF is created
Initial commit
Merge branch 'master' of https://github.com/grossbjo/cuneigatk

Conflicts:
	solution03_variant-call_GATK.cf