VARiD pipeline

VARiD specifications

Information


Unique identifier OMICS_02163
Name VARiD
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data The alignments and the reference files.
Input format SAM,FASTA
Biological technology Life Technologies
Operating system Unix/Linux
Programming languages C
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.0.7f
Stability Stable
Source code URL http://compbio.cs.utoronto.ca/varid/releases/varid-1.0.7f.tar.gz
Maintained Yes

Versioning


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Documentation


Maintainer


  • person_outline Adrian V. Dalca <>

Additional information


http://compbio.cs.utoronto.ca/varid/releases/README

Publication for VARiD

VARiD IN pipeline

2012
PMCID: 3531709
PMID: 23293637
DOI: 10.3389/fimmu.2012.00386

[…] et al., 2010) identifies indels that appear only in hpts near the primers and discards them. the program does not identify indels occurring far from the primers. varscan (koboldt et al., 2009) and varid (dalca et al., 2010) can identify indels, but these programs deal with variability and single nucleotide polymorphism (snp) identification, and do not distinguish between legitimate […]

VARiD institution(s)
Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Computer Science, University of Toronto, Toronto, ON, Canada; Department of Computer Science, Stanford University, Stanford, CA, USA; Scripps Genomic Medicine, The Scripps Research Institute, La Jolla, CA, USA; Donnelly Centre and the Banting and Best Department of Medical Research, University of Toronto, Toronto, ON, Canada
VARiD funding source(s)
Supported by National Sciences and Engineering Research Council (NSERC) of Canada; Mathematics of Information Technology and Complex Systems (MITACS) grant; and Life Technologies (Applied Biosystems).

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