VarScan 2.4.0 – Variant Caller for Short Sequence Reads

VarScan 2.4.0

:: DESCRIPTION

VarScan is a platform-independent, technology-independent software tool for identifying SNPs and indels in massively parallel sequencing of individual and pooled samples. Given data for a single sample, VarScan identifies and filters germline variants based on read counts, base quality, and allele frequencyh. Given data for a tumor-normal pair, VarScan also determines the somatic status of each variant (Germline, Somatic, or LOH) by comparing read counts between samples.

::DEVELOPER

The McDonnell Genome Institute (MGI) at Washington University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / Mac OsX
  • Java

:: DOWNLOAD

 VarScan

:: MORE INFORMATION

Citation:

Koboldt DC, Chen K, Wylie T, Larson DE, McLellan MD, Mardis ER, Weinstock GM, Wilson RK, & Ding L (2009).
VarScan: variant detection in massively parallel sequencing of individual and pooled samples.
Bioinformatics (Oxford, England), 25 (17), 2283-5 PMID:

SegSeq 1.01 – Detect CNVs from Short Sequence Reads

SegSeq 1.01

:: DESCRIPTION

SegSeq is an algorithm to identify chromosomal breakpoints using massively parallel sequence data

::DEVELOPER

the Broad Institute

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 SegSeq

:: MORE INFORMATION

Citation:

Nat Methods. 2009 Jan;6(1):99-103. Epub 2008 Nov 30.
High-resolution mapping of copy-number alterations with massively parallel sequencing.
Chiang DY, Getz G, Jaffe DB, O’Kelly MJ, Zhao X, Carter SL, Russ C, Nusbaum C, Meyerson M, Lander ES.