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Previously known as the Cancer Analysis Workflow (CAW), Sarek is a workflow tool designed to run analyses on WGS data from regular samples or tumour / normal pairs, including relapse samples if required. It's built using Nextflow, a bioinformatics domain specific language for workflow building. Software dependencies are handled using Docker or Singularity - container technologies that provide excellent reproducibility and ease of use. Singularity has been designed specifically for high-performance computing environments. This means that although Sarek has been primarily designed for use with the Swedish UPPMAX HPC systems, it should be able to run on any system that supports these two tools.
dockstore-cgpwgs provides a complete multi threaded WGS analysis for SNV, INDEL, SV and Copynumber variation with associated annotation of VCF files. This has been packaged specifically for use with the Dockstore.org framework. This is intended to be run using the Dockstore.org framework under docker but can be executed as a normal docker container (or imported into singularity.
The Personal Cancer Genome Reporter (PCGR) is a stand-alone software package for functional annotation and translation of individual cancer genomes for precision oncology. It interprets both 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.