Strelka: accurate somatic small-variant calling from sequenced tumor-normal sample pairs

By Christopher T. Saunders, Wendy S. W. Wong, Sajani Swamy, Jennifer Becq, Lisa Murray, R. K. Cheetham, Dr. Michael Brudno. Bioinform., 2012

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A Living Biobank of Breast Cancer Organoids Captures Disease Heterogeneity. (2018, neutral): “0.14) Saunders et al., 2012 ftp://ftp.illumina.com/v1-branch/v1.”
pVAC-Seq: A genome-guided in silico approach to identifying tumor neoantigens (2016, positive): “(3) Strelka version 1.0.10 [35] ( params: isSkip-DepthFilters = 1 ).”
Comprehensive and Integrative Genomic Characterization of Hepatocellular Carcinoma (2017, positive): “Multi-Center Mutation Calling Mutations were called by five production or analysis centers within the TCGA Network: Human Genome Sequencing Center (Comprehensive And Reproducible Nucleotide Alterations in Cancer–CARNAC), UCSC (RADIA), BCGSC (Strelka), and Broad Institute (MuTect) as described below.”
Cell-of-Origin Patterns Dominate the Molecular Classification of 10,000 Tumors from 33 Types of Cancer (2018, background): “As drugs become increasingly clinically available to target such cancer-driving pathway targets as ALK, EGFR, ERBB2, ERα, KIT, BRAF, and ABL1, the traditional system of anatomic cancer classification should be supplemented by a classification system based on molecular alterations shared by tumors ac”
Isaac: ultra-fast whole-genome secondary analysis on Illumina sequencing platforms (2013, methodology): “We also demonstrate that Isaac can successfully detect a clinically deleterious variant in a neonatal sample (Saunders et al., 2012).”