• Fixes CheckIlluminaDirectory problem with cbcl files and skips in the READ_STRUCTURE (#1489)
• Add arguments for inputs and output to the ConvertSequencingArtifactToOxoG command (#1492)
• Fixes LiftoverVCF for indels (again) (#1469)
• Only requiring that the input VCF be indexed if an INTERVAL is provided (#1487)
• Allow more SD inputs to LiftoverIntervals and BedToIntervalList (#1446)
• Improvements to CompareMetrics - Now gives fuller description of differences in metrics. - Added feature to ignore differences in certain metrics. - Added 'fuzzy' metric comparison. - Added ability to output a differences file.