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CHANGELOG.md

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Changelog

All notable changes to the StableLift pipeline.

The format is based on Keep a Changelog.

This project adheres to Semantic Versioning.

[1.1.0] - 2024-10-17

Added

  • Add Delly2-sSV support
  • Add preprocessing script for Strelka2 VCFs to add GT field for Funcotator
  • Add process to split large VCFs to parse in chunks

Changed

  • Standardize annotation workflow to always annotate variants after LiftOver
  • Rename Delly2 to Delly2-gSV
  • Upgrade to score version 1.20

[1.0.0] - 2024-09-10

Added

  • Add workflow for SNV callers (Mutect2, HaplotypeCaller, Strelka2, Muse2, SomaticSniper)
  • Add workflow for SV caller (Delly2)
  • Add pipeline diagram
  • Add reverse liftover (GRCh38 -> GRCh37) for SNV branch
  • Add reverse liftover (GRCh38 -> GRCh37) for SV branch
  • Add optional target_threshold and target_specificity parameters
  • Add NFTest cases for all variant callers and directions

Changed

  • Sort VCF after liftover in SV branch
  • Hide parametric complexity behind simpler user inputs
  • Downgrade to score version 1.16