SV-STAT statistics

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chevron_left Structural variant detection Deletion detection Insertion detection Inter-chromosomal translocation detection Assembly polishing Inversion detection Intra-chromosomal translocation detection chevron_right
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SV-STAT specifications

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Unique identifier OMICS_13029
Name SV-STAT
Alternative name Structural Variation detection by STAck and Tail
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Perl, Python, Shell (Bash)
License GNU General Public License version 3.0
Computer skills Advanced
Stability No
Requirements
Dbfasta, BWA, Picard, Samtools, BioPerl, Bedtools
Source code URL https://gitorious.org/svstat/svstat?p=svstat:svstat.git
Maintained No

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Publication for Structural Variation detection by STAck and Tail

SV-STAT in publication

PMCID: 4496310
PMID: 25569436
DOI: 10.1038/gim.2014.189

[…] to children diagnosed with neoplasms and found to carry apparently balanced constitutional translocations, to discover novel genic disruptions., we applied sv calling programs crest, break dancer, sv-stat and cgap-cnv, and developed an annotative filtering strategy to achieve nucleotide resolution at the translocations., we identified the breakpoints for t(6;12) (p21.1;q24.31) disrupting hnf1a […]


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SV-STAT institution(s)
Structural and Computational Biology and Molecular Biophysics (SCBMB) Program, Baylor College of Medicine, Houston, TX, USA; Texas Children’s Cancer Center, Baylor College of Medicine, Houston, TX, USA; W. M. Keck Center for Interdisciplinary Bioscience Training, Houston, TX, USA; Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA
SV-STAT funding source(s)
This work was supported by the following grants from the NIH: National Institute of General Medical Sciences (K12 GM084897), and a training fellowship from the Keck Center for Interdisciplinary Bioscience Training of the Gulf Coast Consortia (T15 LM007093).

SV-STAT reviews

 (2)
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Ray Cui

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Hello. We have 250x2 PE reads of the insert size ~400bp, and also mate pair libraries of 3kb, 7kb and 10kb inserts. Is it possible to use all of these reads jointly for detecting variations? I am mainly using this to perform a final polishing of our de novo genome assembly (from the same data).
Caleb Davis's avatar image No country

Caleb Davis

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SV-STAT detects genomic rearrangements from NGS data with high accuracy and is complementary to existing tools. It is easy to use and has minimal dependencies.

I am the author of this tool. Please do not hesitate to contact me with any questions.