Update tabix commmand and remove VcfFilAnn
Add seqtk conversion of quality scores, removed F from pipeline
Changes to annotations - added DepthBySampleHC; add filter_mismatching_base_and_quals
Add filter_mismatching_base_and_quals
Changes to info field annotations as some were causing errors. Added a system of log files so that the Merge script can check that the whole completed before it begins merging
Added checks to see if all of the GenotypeGVCFs array job completed
Minor bug fix - spaces in the filterExpressions
Updated annovar database
Updated tabix command with skip argument