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Roslin is a cancer informatics pipeline maintained by the Platform Informatics group at the Center for Molecular Oncology (CMO). Its workflow for targeted-variants is capable of variant calling, annotation, and analysis of data from 341, 410, or 468 gene MSK-IMPACT assays [1], IMPACT+, HemePACT, and various exome capture kits. Additional workflows for xenograft, cell-free DNA, whole genome, and RNA-seq are planned for 2019.
Roslin builds on prior work by the Bioinformatics Core, Clinical Bioinformatics, and Computational Oncology groups, and continues to rely on their accumulated experience and expertise, with emphasis on these features:
Modular - Easily addon or replace sequence aligners, variant callers, false-positive filters, functional/clinical annotation, and analysis modules for manuscript-ready plots/tables.
Reproducible - Retain all older versions and documentation in sufficient detail to reproduce published results, with zero dependencies on proprietary software or obfuscated methods.
Portable - Install Roslin and process new datasets with minimal fuss on laptops, workstations, local compute clusters, or cloud compute servers.
Most of these goals are accomplished using UCSC's Toil [2], a cross-platform workflow management system that uses the Common Workflow Language (CWL), a workflow definition standard promoted by the Global Alliance for Genomics and Health (GA4GH).
- Cheng, D. T., Mitchell, T. N., Zehir, A., Shah, R. H., Benayed, R., Syed, A., ... & Brannon, A. R. (2015). Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT): a hybridization capture-based next-generation sequencing clinical assay for solid tumor molecular oncology. The Journal of molecular diagnostics, 17(3), 251-264.
- Vivian, J., Rao, A. A., Nothaft, F. A., Ketchum, C., Armstrong, J., Novak, A., … Paten, B. (2017). Toil enables reproducible, open source, big biomedical data analyses. Nature Biotechnology, 35(4), 314–316. http://doi.org/10.1038/nbt.3772