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:
If you want to interrogate germline variants and their relation to cancer predisposition, we recommend trying the accompanying tool Cancer Predisposition Sequencing Reporter (CPSR).
May 2022: 1.0.3 release
March 2022: 1.0.2 release
March 2022: 1.0.1 release
February 2022: 1.0.0 release
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-validatorwas often too stringent so its use has been deprecated. The
--no_vcf_validateoption remains for backwards compatibility.
June 30th 2021: 0.9.2 release
November 30th 2020: 0.9.1 release
Learn more about
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
sigven AT ifi.uio.no