github broadinstitute/picard 2.7.2
on GitHub

  • Add tools to be documented + minor tweaks to MD docs
  • Small typo in IlluminaBasecallsToSam doc.
  • Adding an option to output an concordance state annotated VCF in GenotypeConcordance.
  • Fix the same variant returned multiple times by ByIntervalListVariantContextIterator.
  • new CLP: FindMendelianViolations (#536)
  • Fix for MergeBamAlignment when one read maps to both pos and neg strand
  • updating gradle from 2.13 -> 3.1 (#680)
  • - moved FindMendelianViolations from the private repository - added a test - cleaned up the code a-la-java8
  • update htsjdk to 2.7.0 (#681)
  • Include low quality bases in the base quality histogram and add a new coverage histogram that includes these bases in order to improve theoretical het sensitivity estimates.
  • delete unused imports, change year in license
  • rename utils methods in tests
  • add license to tests
  • added tests for both algorithms
  • migrate elc first version of algorithm
3 years ago