• upgrade to htsjdk 2.16.1 (#1224)
• now starting from the origin commit
• Fix output file naming
• Fix to ValidateSamFile to warn when NM validation occurs without reference (#258) (#1220)
• improves MarkDuplcates documentation, fixes #1087 (#1088)
• Installation of r-base in Docker Image allows RExecutor to work (#1198)
• Warning message about upcoming command line syntax transition. (#1204)
• CreateSequenceDictionary support for alternative names (@SQ-AN) (#1127)
• Fix GenotypeConcordance bug writing spanning deletion (#1210)
• The method createTemporaryIndexedVcfFromInput(File, String) was changed (#1213)