sigven/pcgr

Personal Cancer Genome Reporter (PCGR)

Overview

The Personal Cancer Genome Reporter (PCGR) is a stand-alone software package for translation of individual tumor genomes for precision cancer medicine.

PCGR interprets primarily somatic SNVs/InDels and copy number aberrations. The software extends basic gene and variant annotations from the Ensembl's Variant Effect Predictor (VEP) with oncology-relevant, up-to-date annotations retrieved flexibly through vcfanno, and produces interactive HTML reports intended for clinical interpretation. PCGR can perform multiple types of analyses, including:

• Somatic variant classification (ACMG/AMP)
  • mapping the therapeutic and prognostic implications of somatic DNA aberrations
• Tumor mutational burden (TMB) estimation
• Tumor-only analysis (variant filtering)
• Mutational signature analysis
• Kataegis detection
• Microsatellite instability (MSI) classification

If you want to interrogate germline variants and their relation to cancer predisposition, we recommend trying the accompanying tool Cancer Predisposition Sequencing Reporter (CPSR).

News

• February 2023: 1.3.0 release

  • Details at CHANGELOG
  • proritize protein-coding BIOTYPE csq (pr201)
  • expose --pcgrr_conda option to flexibly activate pcgrr env via a non-default pcgrr name
  • cpsr_validate_input.py: refactor for efficient custom gene egrep

• November 2022: 1.2.0 release

  • Keep only autosomal, X, Y, M/MT chromosomes
  • Import bcftools as dependency

• October 2022: 1.1.0 release

  • Remove Docker command wrappers
  • Deprecate --no_docker and --docker_uid CLI options
  • Merged PRs pr192, pr193, pr194, pr196.
  • See CHANGELOG for a few more changes.

• May 2022: 1.0.3 release

  • Merged PR #191

• March 2022: 1.0.2 release

  • Fixed CPSR issue #44

• March 2022: 1.0.1 release

  • Fixed bug for huge input sets that cause JSON output crash
    • huge input variant sets (WGS) are now reduced prior to reporting with R, i.e. exclusion of intronic and intergenic variants, as well as upstream/downstream gene variants (#178).
  • Fixed bug for cases where mutational signature analysis reports > 18 different aetiologies after fitting (#187).
  • CHANGELOG

• February 2022: 1.0.0 release

  • 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 30th 2021: 0.9.2 release

  • Data bundle updates (CIViC, ClinVar, CancerMine, UniProt KB, PFAM)
  • Software upgrades: VEP (104), R v4.1/BioConductor 3.13
  • NEW: TOML configuration removed - all options to PCGR are now command-line based
  • NEW: Feed PCGR with a CPSR report to view key germline findings in the tumor report
  • CHANGELOG
  • Planned for next release: Support for analysis of RNA fusions

• November 30th 2020: 0.9.1 release

  • Data bundle updates (CIViC, ClinVar, CancerMine, UniProt KB)
  • CHANGELOG

Example reports

Getting started

• Installation instructions
• Run through an example
• Learn more about
  • Details regarding PCGR input files, and how they should be formatted
  • Configuration of key settings
  • The types and contents of PCGR output files
  • The variant tier system implemented in PCGR
  • The list of gene and variant annotation resources used in PCGR annotation
• Frequenty asked questions (FAQ)

Citation

If you use PCGR, please cite the publication:

Sigve Nakken, Ghislain Fournous, Daniel Vodák, Lars Birger Aaasheim, Ola Myklebost, and Eivind Hovig. Personal Cancer Genome Reporter: variant interpretation report for precision oncology (2017). Bioinformatics. 34(10):1778--1780. doi:10.1093/bioinformatics/btx817

Contact

sigven AT ifi.uio.no