SigmaP – Rare-Variant Analysis

SigmaP

:: DESCRIPTION

SigmaP is a rare-variant method for detecting disease assoociations in case-control sequencing studies. The Sigma-P statistic aggregates the effects of multiple variant sites by computing a weighted sum of the log p-values per site. Each site is weighted by the inverse of its expected standard deviation (denoted by sigma) of the number of variants in controls. The method is robust against signal noise introduced by a large number of neutral variants and is effective for handling variants with opposite effects.

::DEVELOPER

Wang Lab @ Biostatistics Department

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R

:: DOWNLOAD

 SigmaP

:: MORE INFORMATION

Citation

Genet Epidemiol. 2012 Nov;36(7):675-85. doi: 10.1002/gepi.21662. Epub 2012 Aug 3.
A fast and noise-resilient approach to detect rare-variant associations with deep sequencing data for complex disorders.
Cheung YH1, Wang G, Leal SM, Wang S.

RVsharing 1.7.0 – Computes Estimates of the Probability of Related Individuals Sharing a Rare Variant

RVsharing 1.7.0

:: DESCRIPTION

RVsharing computes the probability that a rare variant is shared by related subjects, given that the variant was observed in any of them.

::DEVELOPER

Alexandre Bureau

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ WIndows/ MacOsX
  • R

:: DOWNLOAD

 RVsharing

:: MORE INFORMATION

Citation

Inferring rare disease risk variants based on exact probabilities of sharing by multiple affected relatives.
Bureau A, Younkin SG, Parker MM, Bailey-Wilson JE, Marazita ML, Murray JC, Mangold E, Albacha-Hejazi H, Beaty TH, Ruczinski I.
Bioinformatics. 2014 Apr 16. pii: btu198.

simuRare 1.1 – Simulating Realistic Genomic Data with Rare Variants

simuRare 1.1

:: DESCRIPTION

simuRare a regression-based algorithm that imputes rare variants in currently available SNP array data, and performs a resampling approachto simulate samples that contain both common and rare SNPs.

::DEVELOPER

The Collaborative Center for Statistics in Science(C2S2)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • R

:: DOWNLOAD

 simuRare

:: MORE INFORMATION

Citation

Genet Epidemiol. 2013 Feb;37(2):163-72. doi: 10.1002/gepi.21696. Epub 2012 Nov 17.
Simulating realistic genomic data with rare variants.
Xu Y1, Wu Y, Song C, Zhang H.

TARV v1 – Tree-based Analysis of Rare Variants

TARV v1

:: DESCRIPTION

TARV is a tree-based method to explore the association between rare variants and complex diseases, and find potential genetic and environmental factors and their interactions.

::DEVELOPER

The Collaborative Center for Statistics in Science(C2S2)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • R

:: DOWNLOAD

 TARV

:: MORE INFORMATION

Citation

Song C. and Zhang H.
TARV: Tree-based Analysis of Rare Variants Identifying Risk Modifying Variants in CTNNA2 and CNTNAP2 for Alcohol Addiction,
Genet Epidemiol. 2014 Sep;38(6):552-9. doi: 10.1002/gepi.21843.

SCORE-Seq 7.1 – Score-Type Tests for Detecting Disease Associations With Rare Variants in Sequencing Studies

SCORE-Seq 7.1

:: DESCRIPTION

SCORE-Seq is a command-line program  for detecting disease associations with rare variants in sequencing studies. The mutation information is aggregated across multiple variant sites of a gene through a weighted linear combination and then related to disease phenotypes through appropriate regression models. The weights can be constant or dependent on allele frequencies and phenotypes. The association testing is based on score-type statistics. The allele-frequency threshold can be fixed or variable. Statistical significance can be assessed by using asymptotic normal approximation or resampling. A detailed description of the methods is given in Lin and Tang (2011). The current release covers binary and continuous traits with arbitrary covariates under case-control and cross-sectional sampling

::DEVELOPER

Danyu Lin

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux

:: DOWNLOAD

 SCORE-Seq

:: MORE INFORMATION

Citation

Lin, D. Y. and Tang, Z. Z. (2011).
A General Framework for Detecting Disease Associations With Rare Variants in Sequencing Studies.
American Journal of Human Genetics, 89, 354-367.

RVFam 1.1 – Rare Variants Association Analyses with Family Data

RVFam 1.1

:: DESCRIPTION

The RVFam package provides functions to perform single SNP association analyses and gene-based tests for continuous, binary and survival traits against sequencing data (e.g. exome chip) using family data.

::DEVELOPER

Ming-Huei Chen <mhchen at bu.edu> and Qiong Yang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows
  • R

:: DOWNLOAD

  RVFam

:: MORE INFORMATION

Citation:

RVFam: An R Package for Rare Variant Association Analysis with Family Data.
Chen MH, Yang Q.
Bioinformatics. 2015 Oct 27. pii: btv609.

RvTests v2.1.0 – Rare Variant Test software for Next Generation Sequencing data

RvTests v2.1.0

:: DESCRIPTION

RvTests is a flexible software package for genetic association studies.

::DEVELOPER

Abecasis Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • C++ Compiler

:: DOWNLOAD

 RvTests

:: MORE INFORMATION

Citation

RVTESTS: an efficient and comprehensive tool for rare variant association analysis using sequence data.
Zhan X, Hu Y, Li B, Abecasis GR, Liu DJ.
Bioinformatics. 2016 May 1;32(9):1423-6. doi: 10.1093/bioinformatics/btw079.

RareVariantVis 2.20.0 – Visualization of Rare Variants in Whole Genome Sequencing data

RareVariantVis 2.20.0

:: DESCRIPTION

RareVariantVis is a new tool for analysis of genome sequence data (including non-coding regions) for both germ line and somatic variants.

::DEVELOPER

Tomasz Stokowy <tomasz.stokowy at k2.uib.no>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / WIndows/ MacOsX
  • R
  • BioConductor

:: DOWNLOAD

 RareVariantVis

:: MORE INFORMATION

Citation

RareVariantVis: new tool for visualization of causative variants in rare monogenic disorders using whole genome sequencing data.
Stokowy T, Garbulowski M, Fiskerstrand T, Holdhus R, Labun K, Sztromwasser P, Gilissen C, Hoischen A, Houge G, Petersen K, Jonassen I, Steen VM.
Bioinformatics. 2016 Jun 10. pii: btw359.

BioBin 2.3.0 – Explore Rare Variant Population Stratification

BioBin 2.3.0

:: DESCRIPTION

BioBin meets a critical need for an improved binning algorithm through the advantage of prior biological knowledge and potential cumulative effects of biologically aggregated RVs. BioBin requires the Library of Knowledge Integration (LOKI), which contains diverse prior knowledge from multiple collections of biological data. BioBin can be used to apply multiple levels of burden collapsing/testing, including: regulatory regions, evolutionary conserved regions, genes, and/or pathways without a need for an external feature file. BioBin aids rare variant analysis by binning variants according to prior biological knowledge.

::DEVELOPER

Ritchie Lab

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 BioBin

:: MORE INFORMATION

Citation

Pac Symp Biocomput. 2013:332-43.
Using BioBin to explore rare variant population stratification.
Moore CB, Wallace JR, Frase AT, Pendergrass SA, Ritchie MD.

KL-Rare – Kullback-Leibler Distance Methods for Detecting Disease Association With Rare Variants

KL-Rare

:: DESCRIPTION

KL-Rare is for performing four tests based on Kullback-Leeibler divergence to assess overall association of a group of common and rare variants with a common disease.

::DEVELOPER

Statistical Genetics and Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows /MacOs
  • R
  • MatLab

:: DOWNLOAD

KL-Rare

:: MORE INFORMATION

Citation

Ann Hum Genet, 79 (3), 199-208 May 2015
Kullback-Leibler Distance Methods for Detecting Disease Association With Rare Variants From Sequencing Data
Asuman S Turkmen 1, Zhifei Yan, Yue-Qing Hu, Shili Lin

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