Summary statistics software tools | Genome-wide association analysis

Imputation of individual level genotypes at untyped markers using an external reference panel of genotyped or sequenced individuals has become standard practice in genetic association studies. Direct imputation of summary statistics can also be…

Imputation of individual level genotypes at untyped markers using an external reference panel of genotyped or sequenced individuals has become standard practice in genetic association studies. Direct imputation of summary statistics can also be valuable, for example in meta-analyses where individual level genotype data are not available.

Provides a method for partitioning heritability from genome-wide association…

Provides a method for partitioning heritability from genome-wide association studies (GWAS) summary statistics while accounting for linked markers. LD SCore regression identified strong enrichment…

Identifies associations between gene expression and complex traits using…

Identifies associations between gene expression and complex traits using summary data from genome-wide association studies (GWAS) and expression quantitative trait locus (eQTL). Then, a heterogeneity…

Allows user to calculate p-values for interaction terms in huge numbers of…

Allows user to calculate p-values for interaction terms in huge numbers of linear regressions in a practical amount of time. pulver can be used as a screening tool for scenarios where the number of…

Estimates variance parameters of a bivariate lineax mixed model (LMM) in the…

Estimates variance parameters of a bivariate lineax mixed model (LMM) in the following context arising in genetics research. BiMM is a computationally efficient implementation of a bivariate linear…

Allows gene-level joint analysis of expression Quantitative Trait Loci (eQTLs)…

Allows gene-level joint analysis of expression Quantitative Trait Loci (eQTLs) in cosmopolitan cohorts. JEPEGMIX is a summary statistics based tool that (i) imputes eQTLs statistics, (ii) infers…

Permits association analysis using multiple traits and a single marker for…

Permits association analysis using multiple traits and a single marker for unrelated individuals. USAT combines the MANOVA and the small subunit (SSU) approach to maximize power. It can compute…

An integrative Bayesian fine-mapping model. RiVIERA-MT includes: 1) the ability…

An integrative Bayesian fine-mapping model. RiVIERA-MT includes: 1) the ability to model epigenomic covariance of multiple related traits; 2) efficient posterior inference of causal configuration; 3)…

Integrates individual level genotype data and summary statistics for…

Integrates individual level genotype data and summary statistics for exploration of genetic architecture of complex phenotypes. The IGESS algorithm is based on variational inference and is developed…

Combines information across all available reference panels to produce estimates…

Combines information across all available reference panels to produce estimates of local genetic correlation structure for summary statistics-based methods in arbitrary populations. Adapt-Mix can be…

A very fast software tool for directly imputing summary statistics of untyped…

A very fast software tool for directly imputing summary statistics of untyped makers from cosmopolitan cohorts without using subject-level genotype data. DISTMIX uses a relevant reference panel to…

A JAVA application for direct imputation of summary statistics allowing for…

A JAVA application for direct imputation of summary statistics allowing for covariates. The proof-of-concept simulations and applications to two real data sets demonstrate the value of DISSCO,…

Identifies specific individuals from limited published associations from the…

Identifies specific individuals from limited published associations from the Wellcome Trust Case Control Consortium (WTCCC) dataset. For GWAS results computed over 25 randomly-selected loci, attack…

A software tool which uses only GWAS summary statistics to i) impute the…

A software tool which uses only GWAS summary statistics to i) impute the summary statistics at unmeasured eQTLs and ii) test for the joint effect of all measured and imputed eQTLs in a gene. Applied…

Estimates the amount of variance in trait explained by typed single nucleotide…

Estimates the amount of variance in trait explained by typed single nucleotide polymorphisms (SNPs) at each single locus on the genome from genome-wide association study (GWAS) summary statistics,…

A software tool for Gaussian imputation from summary association statistics, a…

A software tool for Gaussian imputation from summary association statistics, a type of data that is becoming widely available. This approach accounts for the limited sample size of the reference…

Imputes the summary statistics of untyped variants without first imputing their…

Imputes the summary statistics of untyped variants without first imputing their subject-level genotypes. This is achieved by (i) using the conditional expectation formula for multivariate normal…