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Release notes

Version v1.5.2

  • Fixed bug that did not allow FILTER=.

Version v1.5.1

  • Added datamodel for expansion hunter
  • Allow explicitly setting the header names in tabular formats
  • Allow to set a filter value in an INFO field instead of FILTER

Version v1.5.0

  • Added options to return a VCF file on tabular formats (tsv, md) in sv_wgs_filtering
  • Add sv_validator for validating VCF records based on pydantic VCF models
  • Included several pydantic models for VCF records

Version v1.4.0

  • Add standardization of the new cnv_sv-file from Dragen
  • Remove the cnvLength filter from the cnv-file from Dragen
  • Refactor 'merge'-standardization:
  • merge will now post-process the output of svdb merging.
  • header will just sort the VCF header as the header order is destroyed by many tools.
  • ella will introduce an ELLA compatible variant format

Version v1.3.0

  • Introduce better functionality for making custom filters
  • Changes to utils
  • Allow the "search" relation to filters for doing regex search. Primarily meant for crude searching in the CSQ from VEP. Splitting on , and and require regex to match all parts.
  • Changes to sv_postprocessing allow checking for existence of INFO-fields and setting filter exceptions.

Version v1.2.0

  • Introduce more flexible filtering definitions
  • Changes to standardization
  • Ensure minimal starting position is base 1
  • Add CN from Canvas to the FORMAT field when Canvas is merged with Manta

Version v1.1.0

  • Rescue ACMG_class 4,5 and add ACMG_class column to TSV output

Version v1.0.0

Changes

Breaking change

  • Removes the --print-argument from the Python scripts

New features

  • Directly installs runnable scripts
  • sv_standardizer
  • sv_postprocessing
  • sv_wgs_filtering
  • Moves parsing and formatting of VCFs into src/sv_utils.py
  • Remove non-variants (DRAGEN:REF)
  • Add INFO fields canvasSM, canvasPE, canvasBC to back up FORMAT fields SM, PE, BC. Useful for merging.

Version v0.9.0

Version v0.9.0 of this repository was never released, but is a collection of the Python scripts hardcoded in the following repositories

  • svtools@v0.1.2
  • anno-targets@74a1b0f8a4f7045b8e8a628d059c2c0927e558d3