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

Conda update

• Data updates
• Dockerfile improved with renv framework
• Improved consistency between Docker installation and Conda installation

Dashboard + 2020 update

• New report type output (flexdashboard)
• Multiple data updates
• MutationalPatterns for signature analysis
• Detection of kataegis

CancerMine + CIViC update

v0.8.4

0.8.4 release

ClinVar fix

• moved tumor type to main script
• bundle updates