v2.0.0

• Details in CHANGELOG
  • Massive reference data bundle upgrade, new report layout, oncogenicity classification++
  • Support for Singularity/Apptainer
  • Major data/software updates:
    • Ensembl VEP v112
    • ClinVar (2024-06)
    • CIViC (2024-06-21)
    • GENCODE v46/v19 (GRCh38/GRCh37)
    • CancerMine v50 (2023-03)
    • UniProt KB v2024_03

v1.4.1

What's Changed

• skip favicon for Rmarkdown by @sigven in #210
• Use biocondarised vcf2tsvpy by @pdiakumis in #211

Full Changelog: v1.4.0...v1.4.1

v1.4.0

What's Changed

• Pick trans consequence patch by @sigven in #206
• Use VEP vcf as input to vcf2maf.pl by @sigven in #207
• Better handling of pcgr/pcgrr conda env custom naming by @pdiakumis in #208
• Update report style by @sigven in #209

Full Changelog: v1.3.0...v1.4.0

v1.3.0

CHANGELOG

v1.2.0

CHANGELOG

v1.0.3

Merged #191

v1.0.2

• Fixed JSON crash in CPSR

v1.0.1

• Fixed bug for huge input VCF (JSON output crashes)

v1.0.0

• Complete restructure of Python and R components. Installation now relies on two separate conda packages, pcgr (Python component) and pcgrr (R component). Direct Docker support remains, with the Dockerfile simplified to rely exclusively on the installation of the above Conda packages. Significant contributon by the great @pdiakumis
  • VCF validation step removed. Feedback from users suggested that Ensembl's vcf-validator was often too stringent so its use has been deprecated. The --no_vcf_validate option remains for backwards compatibility.
  • New documentation site (https://sigven.github.io/pcgr)
  • Data bundle updates (CIViC, ClinVar, Open Targets Platform, CancerMine, UniProt KB, Pfam)
  • CHANGELOG

June 2021 release

• Data updates
• Software updates (R, VEP)
• No TOML - all command-line
• Possibility to Add CPSR contents to PCGR reports