Changelog

1.1.1 (10/30/2018)

  • Adjusted Mutect translators to:
    • parse normal and tumor designations from SAMPLE metaheaders if available
    • recognize more variations of Mutect metaheader formats

1.1.0 (6/18/2018)

  • Adjusted translate to correctly parse newer versions of Mutect
  • Updated supported versions for Mutect, Strelka, Varscan
  • Fixed error in JQ_SUMMARY_DP_AVERAGE tag description

1.0.0 (6/5/2018)

  • Removed obsolete spikes directory
  • Fixed bug in expand which could overwrite fixed VCF fields (e.g. REF, ALT, etc.) if identically named fields in INFO.
  • Switched to semantic versioning

0.42 (9/22/2015)

  • 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