Skip to content

Changelog

All notable changes to VNtyper 2 are documented on this page.

2.0.1 (Current)

  • Disabled duplicate flagging in Kestrel configuration.
  • Cleared motifs_for_alt_gg array to prevent unintended variant filtering.
  • Fixed flagging to occur before variant selection, preventing selection of flagged variants (#145).
  • Fixed confidence assignment to filter sub-threshold variants at the root rather than via override.
  • Raised Low_Depth_Conserved_Motifs threshold from 0.2 to 0.4.
  • Updated variant selection to prioritize depth score before haplotype count.
  • Extracted frameshift deduplication into a helper function for clarity.
  • Added comprehensive unit tests for the flagging module.

2.0.0

A complete rewrite and modernization of the VNtyper 2 pipeline.

  • Modern Python packaging using pyproject.toml (PEP 517/518/621).
  • Refactored Kestrel postprocessing with configurable thresholds via kestrel_config.json.
  • HTML reports with embedded IGV integration for interactive variant inspection.
  • Cohort analysis command with built-in pseudonymization for multi-sample studies.
  • Docker multi-stage build for reproducible, lightweight container images.
  • Comprehensive test suite with unit and integration tests, including downloadable test data.
  • Multiple reference assemblies supported: hg19, hg38, GRCh37, and GRCh38.
  • Modular architecture separating variant parsing, motif processing, scoring, flagging, and confidence assignment into individual modules.
  • Snakemake workflow for scalable batch processing.

1.x

The original VNtyper release as described in Saei et al., iScience 2023. This version provided the initial alignment-free genotyping approach for MUC1 VNTR using Kestrel and adVNTR.