maxLRc – Rare Variant Prioritization

maxLRc

:: DESCRIPTION

maxLRc is a likelihood ratio-based measure for the statistical component of ranking rare variants under a case-control study design that avoids the hypothesis-testing paradigm.

::DEVELOPER

Strug lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows/ MacOsX
R

:: DOWNLOAD

maxLRc

:: MORE INFORMATION

Citation

Li W, Dobbins S, Tomlinson I, Houlston R, Pal DK, Strug LJ.
Prioritizing rare variants with conditional likelihood ratios.
Hum Hered. 2015;79(1):5-13. doi: 10.1159/000371579. Epub 2015 Feb 3. PMID: 25659987; PMCID: PMC4759929.

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.

MARRVEL v2 – Model organism Aggregated Resources for Rare Variant ExpLoration

MARRVEL v2

:: DESCRIPTION

MARRVEL aims to facilitate the use of public genetic resources to prioritize rare human gene variants for study in model organisms. To automate the search process and gather all the data in a simple display we extract data from human data bases (OMIM, ExAC, Geno2MP, DGV, and DECIPHER) for efficient variant prioritization. The protein sequences for six organisms (S. cerevisiae, C. elegans, D. melanogaster, D. rerio, M. musculus, and H. sapiens) are aligned with highlighted protein domain information via collaboration with DIOPT.

:: DEVELOPER

Liu Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Wang J, Al-Ouran R, Hu Y, Kim SY, Wan YW, Wangler MF, Yamamoto S, Chao HT, Comjean A, Mohr SE; UDN, Perrimon N, Liu Z, Bellen HJ.
MARRVEL: Integration of Human and Model Organism Genetic Resources to Facilitate Functional Annotation of the Human Genome.
Am J Hum Genet. 2017 Jun 1;100(6):843-853. doi: 10.1016/j.ajhg.2017.04.010. Epub 2017 May 11. PMID: 28502612; PMCID: PMC5670038.

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

Bernie Pope

:: 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.

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.