Changelog

0.42 (X/X/XXXX)

• Added docs on readthedocs.
• Improved workflow documentation with example data
• Merge will now disambiguate tag collisions from multiple VCs
• Translate/summarize now supports GT tags
• Extended precision to 4 decimal places to support analysis of gene-panels.
• Adjusted translate to handle empty high-confidence VarScan files.

0.41 (5/7/2015)

• Combined filter command with merge command
• Extended expand to create simple metaheader glossary
• Adjusted code to support Python >=2.7 or 3.x
• Improved checks for consistent VCF file sets
• Fixed bug in merge that caused error if any VCFs were unsorted
• Fixed bug in summarize that caused error if variant was called by subset of callers

0.31 (3/17/2015)

• Downgraded VCF format from 4.2 to 4.1
• Fixed a bug that omitted CALLERS_REPORTED_LIST summary tag
• Simplified summary tags; removed dependency on numpy
• Adjusted VarScan translation to accept a file pattern to identify high-confidence files

0.3 (3/9/2015)

• Replaced normalize, tag commands with translate; relaxed constraints on incoming data.
• Renamed consensus to summarize
• More consistent behavior in expand
• Significantly improved merge performance
• Added new summary tags: - CALLERS_REPORTED_COUNT - CALLERS_REPORTED_LIST - SAMPLES_REPORTED_COUNT - CALLERS_PASSED_COUNT - CALLERS_PASSED_LIST - SAMPLES_PASSED_COUNT
• Fixed bug in how Strelka calculated AF on indels
• Improved command validation and error handling
• Added project/code documentation
• Removed dependencies on pandas

0.21 (10/2014)

• Initial public release