svtools specifications

Information


Unique identifier OMICS_34193
Name svtools
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
License MIT License
Computer skills Advanced
Stability Stable
Requirements
Numpy, Scipy, Pandas, Statsmodels, SVTyper
Maintained Yes

Download


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Versioning


No version available

Documentation


Maintainer


  • person_outline Ira Hall

Additional information


https://github.com/hall-lab/svtools/blob/master/Tutorial.md

Publications for svtools

svtools citation

library_books

Comprehensive description of genomewide nucleotide and structural variation in short‐season soya bean

2017
Plant Biotechnol J
PMCID: 5814582
PMID: 28869792
DOI: 10.1111/pbi.12825

[…] discover a comprehensive catalogue of SVs from WGS data, we used three tools: LUMPY (Layer et al., ), BreakDancer (Chen et al., ) and CNVnator (Abyzov et al., ). We used SVtyper (Chiang et al., ) and svtools (Larson et al., ) for calling the presence or absence of SVs in individual accessions. The raw calls were filtered for 1) the estimated read‐depth ratio (<0.75), 2) the number of spanning read […]

svtools institution(s)
McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA; Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA; CiBO Technologies, St. Louis, MO, USA; Biofrontiers Institute, University of Colorado, Boulder, CO, USA; Department of Computer Science, University of Colorado, Boulder, CO, USA; Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
svtools funding source(s)
Supported by the National Institutes of Health/National Human Genome Research Institute [grant numbers 5U54HG003079, 1UM1HG008853].

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