RVD 27 – Hierarchical Bayesian model to detect Rare Single Nucleotide Variants

RVD 27

:: DESCRIPTION

RVD2 is an ultra-sensitive variant detection model for low-depth targeted next-generation sequencing data

::DEVELOPER

Flaherty Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • Python

:: DOWNLOAD

 RVD2

:: MORE INFORMATION

Citation

RVD2: An ultra-sensitive variant detection model for low-depth heterogeneous next-generation sequencing data.
He Y, Zhang F, Flaherty P.
Bioinformatics. 2015 Apr 29. pii: btv275.

RAREVATOR – RAre REference VAriant annotaTOR

RAREVATOR

:: DESCRIPTION

RAREVATOR is a tool for the identification and annotation of germline and somatic variants in rare reference allele loci from second generation sequencing data.

::DEVELOPER

RAREVATOR team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 RAREVATOR

:: MORE INFORMATION

Citation:

Characterization and identification of hidden rare variants in the human genome
Magi A, D’Aurizio R, Palombo F, Cifola I, Tattini L, Semeraro R, Pippucci T, Giusti B, Romeo G, Abbate R, Gensini GF.
BMC Genomics. 2015 Apr 24;16(1):340.

FAVR 1.0 – Filtering and Annotation of Variants that are Rare

FAVR 1.0

:: DESCRIPTION

FAVR is a suite of new methods designed to work with commonly used MPS analysis pipelines to assist in the resolution of some of the issues related to the analysis of the vast amount of resulting data, with a focus on relatively rare genetic variants.

::DEVELOPER

FAVR team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Python
  • PySam

:: DOWNLOAD

 FAVR

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2013 Feb 25;14:65. doi: 10.1186/1471-2105-14-65.
FAVR (Filtering and Annotation of Variants that are Rare): methods to facilitate the analysis of rare germline genetic variants from massively parallel sequencing datasets.
Pope BJ1, Nguyen-Dumont T, Odefrey F, Hammet F, Bell R, Tao K, Tavtigian SV, Goldgar DE, Lonie A, Southey MC, Park DJ.

CBrother 2.0 – Infer Recombination when Recombination is Rare

CBrother 2.0

:: DESCRIPTION

cBrother is software for inferring recombination when recombination is rare.

::DEVELOPER

Dorman Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/windows
  • C Compiler

:: DOWNLOAD

 CBrother

:: MORE INFORMATION

Citation

Bioinformatics. 2007 Feb 15;23(4):507-8. Epub 2006 Dec 4.
cBrother: relaxing parental tree assumptions for Bayesian recombination detection.
Fang F, Ding J, Minin VN, Suchard MA, Dorman KS.