Tag: Variant

VNTRseek 1.08 – Detect Tandem Repeat Variants in High-throughput Sequencing data

VNTRseek 1.08

:: DESCRIPTION

VNTRseek is a targeted, effient VNTR (Variable Number of Tandem Repeats) detection software which can provide essential information on VNTR occurrence and characteristics of minisatellites.

::DEVELOPER

Laboratry of Bioinformatcis at Boston University.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 VNTRseek

:: MORE INFORMATION

Citation

VNTRseek-a computational tool to detect tandem repeat variants in high-throughput sequencing data.
Gelfand Y, Hernandez Y, Loving J, Benson G.
Nucleic Acids Res. 2014 Jul 23. pii: gku642.

VPA 0.3.6 – Variant Pattern Analyzer

VPA 0.3.6

:: DESCRIPTION

VPA is an R tool for prioritizing variants with specified frequency pattern from multiple study subjects in next-generation sequencing study.

::DEVELOPER

Qiang Hu (huqmail@gmail.com)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • R

:: DOWNLOAD

 VPA

:: MORE INFORMATION

Citation

BMC Res Notes. 2012 Jan 14;5:31. doi: 10.1186/1756-0500-5-31.
VPA: an R tool for analyzing sequencing variants with user-specified frequency pattern.
Hu Q1, Wang D, Yan L, Zhao H, Liu S.

ABC-GWAS – Analysis of Breast Cancer GWAS variants

ABC-GWAS

:: DESCRIPTION

ABC-GWAS is an interactive database of functional annotation of estrogen receptor-positive breast cancer GWAS variants.

::DEVELOPER

Jun S. Song’s Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

ABC-GWAS

:: MORE INFORMATION

Citation

Manjunath M, Zhang Y, Zhang S, Roy S, Perez-Pinera P, Song JS.
ABC-GWAS: Functional Annotation of Estrogen Receptor-Positive Breast Cancer Genetic Variants.
Front Genet. 2020 Jul 20;11:730. doi: 10.3389/fgene.2020.00730. PMID: 32765587; PMCID: PMC7379852.

PVAAS 0.1.5 – Identify Variants Associated with Aberrant Splicing from RNA-seq

PVAAS 0.1.5

:: DESCRIPTION

PVAAS  (Program to identify Variants Associated with Aberrant Splicing)is a tool to identify single nucleotide variants that associated with aberrant alternative splicing from RNA-seq data.

::DEVELOPER

Liguo Wang: wangliguo78_AT_gmail.com

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • GCC
  • Python

:: DOWNLOAD

 PVAAS

:: MORE INFORMATION

Citation

PVAAS: Identify Variants Associated with Aberrant Splicing from RNA-seq.
Wang L, Nie JJ, A Kocher JP.
Bioinformatics. 2015 Jan 7. pii: btv001.

VIP 1.0 – SNP Variant Detection tool from Pooled DNAs

VIP 1.0

:: DESCRIPTION

VIP (Variant Identification by Pooling)is a complete data analysis framework for  overlapping pool design. It is very flexible and can be combined with any pool design approaches and sequence mapping/alignment tools.

::DEVELOPER

Computational Biology lab @ Case (CBC)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • Perl
  • MatLab

:: DOWNLOAD

 VIP

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Jan 1;29(1):29-38. doi: 10.1093/bioinformatics/bts645. Epub 2012 Oct 27.
Rare variant discovery and calling by sequencing pooled samples with overlaps.
Wang W1, Yin X, Soo Pyon Y, Hayes M, Li J.

CRISP 0.2 – Detection of SNVs and Short Insertion/deletion variants from Pooled high throughput DNA sequencing data

CRISP 0.2

:: DESCRIPTION

CRISP (Comprehensive Read analysis for Identification of Single Nucleotide Polymorphisms from Pooled sequencing) is a software program to detect SNPs and short indels from pooled sequencing data generated using next-generation sequencing instruments. CRISP is designed to detect both rare and common variants by utilizing sequence reads from next-generation sequencing of multiple DNA pools.

::DEVELOPER

Bansal Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  •  Linux

:: DOWNLOAD

 CRISP 

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Jun 15;26(12):i318-24. doi: 10.1093/bioinformatics/btq214.
A statistical method for the detection of variants from next-generation resequencing of DNA pools.
Bansal V.

CAVIAR – CAusal Variants Idenfitication in Associated Regions

CAVIAR

:: DESCRIPTION

CAVIAR , a statistical framework that quantifies the probability of each variant to be causal while allowing with arbitrary number of causal variants.

:: DEVELOPER

CAVIAR team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / WIndows
  • Python / C

:: DOWNLOAD

 CAVIAR

:: MORE INFORMATION

Citation

Genetics. 2014 Oct;198(2):497-508. doi: 10.1534/genetics.114.167908. Epub 2014 Aug 7.
Identifying causal variants at loci with multiple signals of association.
Hormozdiari F, Kostem E, Kang EY, Pasaniuc B, Eskin E

GenomeVIP v1.2.1 – Cloud based Genome Variant Investigation Platform

GenomeVIP v1.2.1

:: DESCRIPTION

GenomeVIP is a web application platform for performing variant discovery on Amazon’s Web Service (AWS) cloud or on local high-performance computing clusters.

::DEVELOPER

Ding Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

GenomeVIP

:: MORE INFORMATION

Citation

Mashl RJ, Scott AD, Huang KL, Wyczalkowski MA, Yoon CJ, Niu B, DeNardo E, Yellapantula VD, Handsaker RE, Chen K, Koboldt DC, Ye K, Feny? D, Raphael BJ, Wendl MC, Ding L.
GenomeVIP: a cloud platform for genomic variant discovery and interpretation.
Genome Res. 2017 Aug;27(8):1450-1459. doi: 10.1101/gr.211656.116. Epub 2017 May 18. PMID: 28522612; PMCID: PMC5538560.

Kaviar 160204- Queryable database of known Variants

Kaviar 160204

:: DESCRIPTION

Kaviar is a compilation of human SNVs collected from many and diverse sources, stressing accessibility and ease of use. Kaviar (~Known VARiants) is a very simple tool for answering a very specific question: What variants have been reported already for a given specific genomic location?

::DEVELOPER

Gustavo Glusman

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Server
  • Perl

:: DOWNLOAD

 Kaviar

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Nov 15;27(22):3216-7. doi: 10.1093/bioinformatics/btr540. Epub 2011 Sep 28.
Kaviar: an accessible system for testing SNV novelty.
Glusman G, Caballero J, Mauldin DE, Hood L, Roach JC.

NGS-eval – NGS Error Analysis and VAriant Detection tooL

NGS-eval

:: DESCRIPTION

NGS-eval is an interactive web server for error analysis and sequence variant detection in amplicon-based NGS mock (or marker gene) data sets.

::DEVELOPER

The Centre for Integrative Bioinformatics VU

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

NGS-eval: NGS Error analysis and novel sequence VAriant detection tooL.
May A, Abeln S, Buijs MJ, Heringa J, Crielaard W, Brandt BW.
Nucleic Acids Res. 2015 Apr 15. pii: gkv346.