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@d-cameron d-cameron released this 11 Aug 12:45
· 95 commits to master since this release
v2.12.1
989e0f0

DO NOT USE: this release has a critical bug in the preprocessing step that removes all split reads

Minor feature and bug fix release.

A pre-built VIRUSBreakend database is now available from [here].(https://github.com/PapenfussLab/gridss/blob/master/VIRUSBreakend_Readme.md#reference-data).

GRIDSS

  • gridss with no arguments now prints the usage message as intended
  • #511 AF VCF FORMAT field now populated
  • #513 Added --skipsoftcliprealignment option
    • Reduces runtime when using an aligner that already reports split reads (e.g. bwa)
  • Ignoring imprecise deletion-like calls less than 500bp in size.
    • Very high coverage samples have a high rate of small FP DEL calls caused by fragments slightly longer than the (99%) maximum expected fragment size
  • Fixed non-deterministic assembly SAM tag evidence ordering
  • #503 limiting error reproduction packages to 5.
    • configurable with assembly.maximumReproductionExportPackages
  • #503 stripping SAM "aa" tag from input reads
  • Fixed crash bug in SAMRecordUtil.ByBestPrimarySplitCandidate
  • Added libdeflate to gridsstools
  • Added --no-PG to samtools sort so BAM outputs are deterministic
  • #509 improved gridss_somatic_filter script path determination so it works in the Docker image
  • Added LICENSE to release package to remove bioconda lint warning

VIRUSBreakend

  • #508 using RefSeq viral genome whenever available
  • #504 Fixed rname header separator in VIRUSBreakend .summary.tsv output
  • #499 running gridss preprocess so annotation doesn't fail
  • #499 Including edirect setup step in docker image
  • #499 added bcftools to the Docker image
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