SomaticSniper: identification of somatic point mutations in whole genome sequencing data

By David E. Larson, C. Harris, Ken Chen, Daniel C. Koboldt, Travis E. Abbott, D. Dooling, T. Ley, Elaine R. Mardis, Richard K. Wilson, Li Ding. Bioinform., 2012

636 citations recorded by the source corpus.

Subfields: Cancer Research, Genetics, Pathology and Forensic Medicine

View Paper: https://www.semanticscholar.org/paper/fe9a3f2ce59442eca7c2708869fb3a685ad16620

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In Pathology and Forensic Medicine

Citations in the corpus

A Recurrent Mutation in Anaplastic Lymphoma Kinase with Distinct Neoepitope Conformations (2018, background): “Somatic point mutations were called using a panel of five mutation callers, MuTECT (63), MuSE (64), RADIA (65), SomaticSniper (66), and Strelka (67).”
Tumor and Microenvironment Evolution during Immunotherapy with Nivolumab (2017, neutral): “13.0 Roth et al., 2014; PMID: 24633410 http://compbio.bccrc.ca/software/pyclone/ SOAP-HLA Short Oligonucleotide Analysis Package http://soap.genomics.org.cn/SOAP-HLA.html SomaticSniper 1.0.4 Larson et al., 2012; PMID: 22155872 https://github.com/genome/somatic-sniper/ releases/tag/v1.”
The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma (2018, methodology): “…the capstone project using all available of cases within TCGA using six different algorithms (MuTect, MuSE, Pindel, Somatic Sniper, VarScan2 and Radia) from four centers (Cibulskis et al., 2013; Fan et al., 2016; Koboldt et al., 2012; Larson et al., 2012; Radenbaugh et al., 2014; Ye et al., 2009).”
Toward better understanding of artifacts in variant calling from high-coverage samples (2014, background): “In addition, only a few works (Larson et al., 2012; Roberts et al., 2013; Kim and Speed, 2013) have attempted to identify the sources of errors.”
Comprehensive and Integrated Genomic Characterization of Adult Soft Tissue Sarcomas. (2017, neutral): “0.4 Larson et al., 2012 RRID:SCR_005108; http://gmt.genome.wustl.edu/ somatic-sniper/current/ Strelka v0.”
pVAC-Seq: A genome-guided in silico approach to identifying tumor neoantigens (2016, methodology): “The filtered Samtools variant calls were intersected with those from Somatic Sniper [32] version 1.0.2 (params: -”
The origin and evolution of mutations in Acute Myeloid Leukemia (2012, methodology): “Somatic SNVs were identified by using SomaticSniper as previously described (Ding et al., 2012; Larson et al., 2012).”
SpeedSeq: Ultra-fast personal genome analysis and interpretation (2014, methodology): “Using this evaluation paradigm, we compared SpeedSeq’s performance to three other leading somatic variant calling tools: MuTect[22], SomaticSniper[23], and VarScan 2[24].”
Calling Somatic SNVs and Indels with Mutect2 (2019, methodology): “([6])Due to an unforeseen unavailability of TCGA data on the cloud for several months we have not yet been able to do this.”
Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection (2015, neutral): “3 and 4 ).”
Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples (2013, neutral): “SomaticSniper and JointSNVMix use a model based on a clonal mutation in a pure, diploid tumor (and thus assume a fixed 50% allele fraction).”
VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. (2012, methodology): “To investigate this possibility, we determined the fraction of mutations called in each set that were also detected in the WGS data by a different algorithm, named SomaticSniper (Larson et al. 2011).”