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-validator
was often too stringent so its use has been deprecated. The --no_vcf_validate
option 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