PriVar – Prioritizing SNVs and Indels from Next-generation Sequencing data

PriVar

:: DESCRIPTION

PriVar is a cross-platform Java application toolkit to prioritize variants (SNVs and InDels) from exome or whole genome sequencing data by using different filtering strategies and information of external databases.

::DEVELOPER

WANLING YANG’S GROUP IN BIOINFORMATICSUniversity of Hong Kong

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

 PriVar

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Jan 1;29(1):124-5. doi: 10.1093/bioinformatics/bts627. Epub 2012 Oct 25.
PriVar: a toolkit for prioritizing SNVs and indels from next-generation sequencing data.
Zhang L1, Zhang J, Yang J, Ying D, Lau YL, Yang W.

BioMuta 4.0 – Single-nucleotide Variations (SNVs) in Cancer

BioMuta 4.0

:: DESCRIPTION

BioMuta is a single-nucleotide variation (SNV) and disease association database where variations are mapped to genomes and RefSeq nucleotide entries, and unified through UniProtKB/Swiss-Prot positional coordinates.

::DEVELOPER

High-performance Integrated Virtual Environment (HIVE)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Database (Oxford). 2014 Mar 25;2014:bau022. doi: 10.1093/database/bau022. Print 2014.
A framework for organizing cancer-related variations from existing databases, publications and NGS data using a High-performance Integrated Virtual Environment (HIVE).
Wu TJ1, Shamsaddini A, Pan Y, Smith K, Crichton DJ, Simonyan V, Mazumder R.

CRISP 20131227 – Detection of SNVs and Short Insertion/deletion variants from Pooled high throughput DNA sequencing data

CRISP 20131227

:: 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

Vikas Bansal

:: 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.