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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

 (28)
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

[…] nt 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 distinguishing somatic and germline. SNVMix2’s, like JointSNVMix2 and Virmid, infers the posterior probability of each genotype. Shearwater is s […]

library_books

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

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

[…] y Illumina GAII or Illumina HiSeq2000. Sequencing reads were aligned and processed by Picard analysis pipeline (http://broadinstitute.github.io/picard/). Variants and AFs were called using Syzygy and SNVer. We used ANNOVAR to annotate variants for RefSeq genes (hg19), GERP scores, ENCODE DHS cluster, and 1000 G data. […]

library_books

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

[…] and 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 that integrate […]

call_split

Alternative Evolutionary Paths to Bacterial Antibiotic Resistance Cause Distinct Collateral Effects

2017
Mol Biol Evol
PMCID: 5850482
PMID: 28541480
DOI: 10.1093/molbev/msx158
call_split See protocol

[…] picard/; 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 in the […]

call_split

Sequencing of cancer cell subpopulations identifies micrometastases in a bladder cancer patient

2017
Oncotarget
PMCID: 5542213
PMID: 28487492
DOI: 10.18632/oncotarget.17312
call_split See protocol

[…] ignment, base quality score recalibration, and removal of duplicate reads were performed using GATK and Picard. Single nucleotide variations (SNV) and INDELs were independently detected by MuTect and SNVer. […]

library_books

Sequence analysis of pooled bacterial samples enables identification of strain variation in group A streptococcus

2017
Sci Rep
PMCID: 5374712
PMID: 28361960
DOI: 10.1038/srep45771

[…] y allelic variations in the two pools, we first mapped the sequence reads to the reference genome and then used four different variant calling tools, SAMtools, Freebayes, GATK’s UnifiedGenotyper, and SNVer. We decided to use more than one variant calling tool, owing to the reported low concordance between different variant calling methods. We utilized variants identified from the six individually […]

Citations

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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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