SomaticSniper statistics

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Citations per year

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Protocols

SomaticSniper specifications

Information


Unique identifier OMICS_00092
Name SomaticSniper
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Programming languages C
License MIT License
Computer skills Advanced
Version 1.0.5.0
Stability Stable
Maintained Yes

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Publication for SomaticSniper

SomaticSniper citations

 (55)
library_books

Genetic Alterations in Essential Thrombocythemia Progression to Acute Myeloid Leukemia: A Case Series and Review of the Literature

2018
PMCID: 5826070
PMID: 29515972
DOI: 10.3389/fonc.2018.00032

[…] nted in the GATK. After alignment, PCR duplication rates and percent reads mapped on target were used to assess the quality of the data. Somatic single nucleotide variants (SNVs) were genotyped using SomaticSniper(), whereas insertions and deletions were called by GATK Somatic Indel Detector. Each variant in coding regions was functionally annotated by snpEFF and PolyPhen-2 () to predict biologica […]

library_books

A review of somatic single nucleotide variant calling algorithms for next generation sequencing data

2018
Comput Struct Biotechnol J
PMCID: 5852328
PMID: 29552334
DOI: 10.1016/j.csbj.2018.01.003

[…] ormal. If RNA-seq data from the same patient are available, RADIA will include the gene expression data in an integrated analysis to further reduce false positives.Joint genotype analysis, adopted by SomaticSniper, FaSD-somatic, SAMtools, JointSNVMix2, Virmid, SNVSniffer, Seurat, and CaVEMan , , , , , , , , assumes diploidy in both tumor and normal and evaluates the likelihood of the joint genotyp […]

call_split

Loss of function uORF mutations in human malignancies

2018
Sci Rep
PMCID: 5799362
PMID: 29402903
DOI: 10.1038/s41598-018-19201-8
call_split See protocol

[…] nocarcinoma samples. Variant allele frequencies were available for 492 sample pairs originating from 433 individual cancers and normal tissue controls, respectively. Four different SNP calling tools (SomaticSniper at http://gmt.genome.wustl.edu/packages/somatic-sniper/, VarScan2 at http://dkoboldt.github.io/varscan/index.html, MuTect2 at https://software.broadinstitute.org/gatk/gatkdocs/org_broadi […]

library_books

A Recurrent Mutation in Anaplastic Lymphoma Kinase with Distinct Neoepitope Conformations

2018
Front Immunol
PMCID: 5797543
PMID: 29441070
DOI: 10.3389/fimmu.2018.00099

[…] aplotype for a sample is decided based on a consensus decision of the three input haplotypes. Somatic point mutations were called using a panel of five mutation callers, MuTECT (), MuSE (), RADIA (), SomaticSniper (), and Strelka (). Since most mutation callers are DNA centric, we allow mutations rejected by up to two of the callers through this first filter. The vcf of first-pass mutants is subje […]

call_split

Comparative genomic analysis of esophageal squamous cell carcinoma between Asian and Caucasian patient populations

2017
Nat Commun
PMCID: 5688099
PMID: 29142225
DOI: 10.1038/s41467-017-01730-x
call_split See protocol

[…] ajor steps included marking duplicates, local realignment around high-confidence insertion and deletions and base quality recalibration. We then used several popular callers, including Muse, MuTect2, SomaticSniper, Radia, and VarScan2, to identify somatic point mutations. Only mutations reported by at least two callers were used in further analyses. Low coverage and strand-biased mutations were fi […]

library_books

Comprehensive benchmarking of SNV callers for highly admixed tumor data

2017
PLoS One
PMCID: 5636151
PMID: 29020110
DOI: 10.1371/journal.pone.0186175

[…] Previous studies also reported that somatic callers tend to identify a small, common set of high-confidence core mutations [, ] combined with an idiosyncratic set of either false positives (VarScan2, SomaticSniper) or low-frequency true positive mutations (MuTect, Strelka) []. A popular caller, VarScan2, has difficulties with detecting lower-frequency mutations [, , ], often calls germline mutatio […]


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SomaticSniper institution(s)
The Genome Institute, Washington University, St Louis, MO, USA; Department of Genetics, Washington University, St Louis, MO, USA; Department of Internal Medicine, Division of Oncology, Washington University, St Louis, MO, USA; Siteman Cancer Center, Washington University, St Louis, MO, USA
SomaticSniper funding source(s)
Supported by National Human Genome Research Institute [grant number HG003079].

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