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CHANGELOG.md

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Changelog

version 1.3.0

  • Added a workflow for somatic SV calling using GRIDSS, delly and manta.
  • Clever is now disabled by default. It can be enabled by setting SVcalling.runClever to true.
  • Fixed a bug which led to the removal of all BND, INS and INV events if DUPHOLD was enabled.
  • Updated SURVIVOR version to 1.0.7.
  • Added a workaround for a bug in survivor which caused the END of events detected by CLEVER to be calculated incorrectly resulting in incorrect merging of events.
  • The gridss outputs are now included in survivor as well.
  • Smoove can now be disabled, by setting SVcalling.runSmoove to false.
  • Added Gridss as SV caller.
  • Fix order of input VCF files when removing missing and homozygous reference genotypes.
  • Each SV type has now seperate temporary directory during sorting.
  • Both union and intersection from each SV types are generated.
  • The pipeline now first seperate SVs by types before merging.
  • Duphold can now be run optionally to annotate and remove FP deletions and duplications.
  • Replace excludeFpDupDel-option with runDuphold-option: DupHold annotation and FP filtering are now optional together.
  • Update CLEVER dockerimage.
  • DELLY: Update docker image.

version 1.2.0

  • Structural-variantcalling pipeline: Remove GRIDSS from the pipeline.
  • Exclude GRIDSS from SURVIVOR merging: SVs were only defined as BNDs in GRIDSS.
  • Optional filtering of missing and hom-ref genotypes.
  • Optional filtering of FP deletions and duplications.
  • Add DUPHOLD: annotate SVs with depth values.
  • Make bcftools indexing optional.
  • Structural-variantcalling pipeline: add sorting and change id.
  • Added GRIDSS sv caller

version 1.1.0

  • Bcftools samtools and picard images are updated to newer versions.
  • Bcftools view now converts delly vcf to a gzipped version.
  • Tasks were updated to contain the time_minutes runtime attribute and associated timeMinutes input, describing the maximum time the task will take to run.

version 1.0.0

  • Add WDL task for smoove SV-caller.
  • Created a structural variant-calling pipeline.