SomaticSniper protocols

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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 in pipelines

 (2)
2016
PMCID: 4741064
PMID: 26855855
DOI: 10.7717/peerj.1508

[…] the new bam file. we used gatk () to do indel realignment and base recalibration, according to the standard best practices for genomics data (). finally, we predicted somatic variants with somaticsniper (), with the output given in vcf format. 10.7717/peerj.1508/fig-1figure 1, for all alignments, average read coverage was 30x, with a low of 5x and a high of 60x (stdev = 15.95898). […]

2015
PMCID: 4460593
PMID: 26045178
DOI: 10.1186/1755-8794-8-S2-S4

[…] × 100-bp paired-end sequencing reads were produced after elution from capture arrays. illumina paired-end reads were aligned to ncbi build36 using bwa 0.5.5. somatic mutations were identified using somaticsniper and a modified version of the samtools indel caller. the tcga data set has 494 variants identified in 50 patients with acute myeloid leukemia (aml) by targeted resequencing of 601 genes […]


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SomaticSniper in publications

 (70)
PMCID: 5951856
PMID: 29760388
DOI: 10.1038/s41467-018-04008-y

[…] allele at the current position, then the position was deemed homozygous reference and no further analysis was performed. the genotype likelihoods were used in a bayesian model used by the somaticsniper method–, incorporating a prior probability on the reference, the fraction of heterozygous positions in the human genome, the probability to convert the normal genotype to the tumor […]

PMCID: 5862875
PMID: 29563506
DOI: 10.1038/s41408-018-0062-y

[…] of a subset of 15 pairs). reads were aligned against human reference genome grch37-lite using bwa. acquired snvs were called in each tumor sample relative to its paired normal sample using samtools, somaticsniper, mutect, strelka, and varscan2 (ref. ). translocations were called using lumpy, with results filtered by a machine learning approach optimized to achieve high precision relative […]

PMCID: 5856809
PMID: 29549256
DOI: 10.1038/s41467-018-03494-4

[…] by the tcga research network (http://cancergenome.nih.gov/) was downloaded from the genomic data commons repository through tcgabiolinks r package., snp calls from muse, mutect, varscan and somaticsniper were combined and filtered for nonsense mutations in the gene apc. (a patient was selected if at least 1 algorithm indicated that apc gene had a nonsense mutation.) expression values […]

PMCID: 5852328
PMID: 29552334
DOI: 10.1016/j.csbj.2018.01.003

[…] 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 […]

PMCID: 5799362
PMID: 29402903
DOI: 10.1038/s41598-018-19201-8

[…] identified uorf-mutations in blk, ephb1, jak2, and map2k6 were covered by ten or more reads in 6, 44, 438, and 141 cancer samples, respectively. none of four independent snp calling tools (somaticsniper, varscan2, mutect2, and muse) detected additional cases of these variants in the extended colon cancer sample set (data not shown). given the high coverage for the jak2 and map2k6 uorf […]


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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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