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@droazen droazen released this 02 Mar 19:41
· 1467 commits to master since this release
4.0.2.1
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Learn about vigilant mode.

This is a small bug fix release containing fixes for the following issues:

  • HaplotypeCaller: fix the -contamination/-contamination-file arguments, which were not working properly, and add tests (#4455)
  • Fixes/improvements to the GATK configuration file mechanism (#4445)
    • If a Java system property is specified explicitly on the user's command line, allow it to override the corresponding value in the GATK config file
    • Bundle an example GATK configuration file with the GATK binary distribution. This config file can be edited and passed to the GATK via the --gatk-config-file argument.
    • There are still some configuration-related TODOs/known issues: in particular, the gatk front-end script currently bakes in some system properties internally, which will always override the corresponding values in the config file. We plan to patch the gatk script to no longer set these system properties internally, and delegate to the config file instead.
  • Mutect2: minor bug fixes and improvements (#4466)
    • Fix "FilterMutectCalls trips on non-int value in MFRL tag" (#4363)
    • Fix ordering of allele trimming vs. variant annotation (#4402)
    • Fix "CalculateContamination gives >100% results" (#3889)
    • Disable the MateOnSameContigOrNoMappedMateReadFilter by default (#3514)
    • Make mapping quality threshold in GetPileupSummaries modifiable (#4011)
  • SV Tools: Add a scan for intervals of high depth, and exclude reads from those regions from SV evidence (#4438)
  • In the GATK docker image, run the GATK using the fully-packaged binary distribution jars, rather than the unpackaged jars (#4476). This fixes a number of minor issues reported by users of the docker image.
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