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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
- Documentation: http://snver.sourceforge.net/snvergui/HelpManual.pdf
Maintainer
- person_outline Zhi Wei
Additional information
Publications for SNVer
SNVer: a statistical tool for variant calling in analysis of pooled or individual next-generation sequencing data.
SNVer citations
(28)A review of somatic single nucleotide variant calling algorithms for next generation sequencing data
[…] 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 […]
Integrating evolutionary and regulatory information with a multispecies approach implicates genes and pathways in obsessive compulsive disorder
[…] 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. […]
Establishing a colorectal cancer liver metastasis patient derived tumor xenograft model for the evaluation of personalized chemotherapy
[…] 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 […]
Alternative Evolutionary Paths to Bacterial Antibiotic Resistance Cause Distinct Collateral Effects
[…] 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 […]
Sequencing of cancer cell subpopulations identifies micrometastases in a bladder cancer patient
[…] 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. […]
Sequence analysis of pooled bacterial samples enables identification of strain variation in group A streptococcus
[…] 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 […]
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