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Protocols

SNVer specifications

Information


Unique identifier OMICS_00076
Name SNVer
Alternative name SNVerGUI
Software type Package/Module
Interface Command line interface, Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Computer skills Advanced
Version 0.5.3
Stability Stable
Maintained Yes

Subtool


  • SNVerPool

Versioning


No version available

Documentation


Maintainer


  • person_outline Zhi Wei <>

Additional information


A Graphical User Interface is available at http://snver.sourceforge.net/snvergui/

Publications for SNVer

SNVer citations

 (36)
library_books

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

2018
PMCID: 5852328
PMID: 29552334
DOI: 10.1016/j.csbj.2018.01.003

[…] mutect and vardict, accept single sample as input (). in addition, several algorithms are dedicated to perform single-sample variant calling. these algorithms include snvmix2, shearwater, splinter, snver, outlyzer, pisces, isown, somvarius, and sinvict , , , , , , , , and fall into two categories., snvmix2, shearwater, splinter, snver, outlyzer, and pisces report all variants without […]

library_books

Whole Genome Sequencing of Suppressor DNA Mixtures Identifies Pathways That Compensate for Chromosome Segregation Defects in Schizosaccharomyces pombe

2018
PMCID: 5844291
PMID: 29352077
DOI: 10.1534/g3.118.200048

[…] tool (v3.00.02; http://www.novocraft.com) with default settings. resulting sam files were converted to bam, and were then sorted and indexed with samtools (v0.1.18; ). mutations were called by snver (v0.5.3; ). since each mixture contains genomic dna of 10 revertants, 10 (or fewer) suppressor mutations, in addition to the original ts mutation, should be identified, with suppressor allele […]

call_split

Alternative dominance of the parental genomes in hybrid cells generated through the fusion of mouse embryonic stem cells with fibroblasts

2017
PMCID: 5741742
PMID: 29273752
DOI: 10.1038/s41598-017-18352-4
call_split See protocol

[…] in gene expression levels., the genes were distributed into categories according to the criteria explained in the results section using homemade python scripts., snp calling was performed using snver software and the mm10 genome as a reference sequence. after calling, all heterozygous snps in the parental m5s and tau-gfp transcriptomes were filtered out. the resulting 27,962 snps were used […]

library_books

Integrating evolutionary and regulatory information with a multispecies approach implicates genes and pathways in obsessive compulsive disorder

2017
PMCID: 5645406
PMID: 29042551
DOI: 10.1038/s41467-017-00831-x

[…] . ), sufficient to identify variants occurring in just one individual, assuming 0.5–1% per base machine error rate., we called 124,541 single nucleotide polymorphisms (snps) using syzygy (84,216) and snver (81,829). for primary analyses, we focused on 41,504 “high-confidence” snps detected by both, with highly correlated allele frequencies (af) (pearson’s ρ = 0.999, p < 2.2 × 10−16; supplementa […]

call_split

Establishing a colorectal cancer liver metastasis patient derived tumor xenograft model for the evaluation of personalized chemotherapy

2017
PMCID: 5658298
PMID: 29094026
DOI: 10.4174/astr.2017.93.4.173
call_split See protocol

[…] recalibration, was performed using gatk best practice of broad institute []., at the variant discovery step, the snvs and indels utilized 3 open source callers (unifiedgenotyper [], lofreq [], and snver []) and samsung sds's in-house callers. cnv and translocation were discovered with in-house callers developed by samsung sds. snvs and indels were detected with an ensemble method […]

library_books

Alternative Evolutionary Paths to Bacterial Antibiotic Resistance Cause Distinct Collateral Effects

2017
PMCID: 5850482
PMID: 28541480
DOI: 10.1093/molbev/msx158

[…] last accessed may 19, 2017). to call snps and small indels above a threshold frequency of 0.1 and base quality above 20, we employed both frequentist and heuristic methods using respectively snver and varscan (; ). to identify larger indels and other sv, we used pindel and cnvnator (; ). the resulting output files were filtered for duplicates, ancestral variants, and variants found […]


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SNVer institution(s)
Department of Computer Science, New Jersey Institute of Technology, Newark, NJ, USA; The Centre for Applied Genomics (TCAG), the Hospital for Sick Children, Toronto, Canada; Center for Applied Genomics, the Children's Hospital of Philadelphia, Department of Pediatrics, University of Pennsylvania, Philadelphia, PA, USA

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