SV-STAT specifications

Information


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 Stable
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 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.