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Fine mapping software tools | Genome-wide association analysis

The goal of fine-mapping in genomic regions associated with complex diseases and traits is to identify causal variants that point to molecular mechanisms behind the associations.Source text:(Benner et al., 2016) FINEMAP: efficient variable selection…
gwasMP
Web

gwasMP

Queries users’ results with different thresholds of physical distance and/or…

Queries users’ results with different thresholds of physical distance and/or Linkage Disequilibrium (LD). gwasMP is an online method for quantifies the physical distance, LD and difference in Minor…

RiVIERA
Desktop

RiVIERA Risk Variant Inference using Epigenomic Reference Annotations

A Bayesian framework to model genome-wide association study (GWAS) summary…

A Bayesian framework to model genome-wide association study (GWAS) summary statistics in terms of P-values using large-scale reference datasets. The main novelty of RiVIERA is the ability to perform…

HAPRAP
Desktop

HAPRAP HAPlotype Regional Association analysis Program

An approach for statistical fine mapping using meta-analysis summary…

An approach for statistical fine mapping using meta-analysis summary statistics. HAPRAP uses haplotypes to represent linkage disequilibrium (LD) structure among multiple variants in a region.…

CAVIAR
Desktop

CAVIAR CAusal Variants Identification in Associated Regions

A method that is able to operate across large LD regions of the genome while…

A method that is able to operate across large LD regions of the genome while also correcting for population structure. A key feature of this approach is that it provides as output a minimally sized…

PAINTOR
Desktop

PAINTOR Probabilistic Annotation INtegraTOR

A probabilistic framework that integrates association strength with functional…

A probabilistic framework that integrates association strength with functional genomic annotation data to improve accuracy in selecting plausible causal variants for functional validation. A key…

CAVIARBF
Desktop

CAVIARBF CAVIAR Bayes Factor

A fine-mapping method using marginal test statistics in the Bayesian framework.…

A fine-mapping method using marginal test statistics in the Bayesian framework. An advantage of the Bayesian framework is that it can answer both association and fine-mapping questions. We used…

FINEMAP
Desktop

FINEMAP

A software package to efficiently explore a set of the most important causal…

A software package to efficiently explore a set of the most important causal configurations of the region via a shotgun stochastic search algorithm. FINEMAP produces accurate results in a fraction of…

GUESSFM
Desktop

GUESSFM

Statistical approaches to this fine mapping problem have traditionally taken a…

Statistical approaches to this fine mapping problem have traditionally taken a stepwise search approach, beginning with the most associated variant in a region, then iteratively attempting to find…

SFBA
Desktop

SFBA Scalable Functional Bayesian Association

Produces enrichment parameter estimate that can help with interpretation of…

Produces enrichment parameter estimate that can help with interpretation of association results. SFBA is a scalable Bayesian hierarchical method for integrating functional information in genome-wide…

PINES
Web

PINES Phenotype-Informed Noncoding Element Scoring

Evaluates the functional impact of noncoding variants by integrating diverse…

Evaluates the functional impact of noncoding variants by integrating diverse epigenetic annotations. PINES directs the analysis towards genomic annotations most relevant to phenotypes of interest. It…

GUESS
Desktop

GUESS Graphical processing Unit Evolutionary Stochastic Search

A computationally optimised C++ implementation of a fully Bayesian variable…

A computationally optimised C++ implementation of a fully Bayesian variable selection approach that can analyse, in a genome-wide context, single and multiple responses in an integrated way. The…

BLIMP
Desktop

BLIMP Best Linear IMPutation

A free software package for imputing allele frequencies from pooled or…

A free software package for imputing allele frequencies from pooled or summary-level genetic data. This approach, which predicts each allele frequency using a linear combination of observed…

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