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Genotype imputation software tools | Genome-wide association analysis

Genotype imputation has been widely adopted in the postgenome-wide association studies (GWAS) era. Owing to its ability to accurately predict the genotypes of untyped variants, imputation greatly boosts variant density, allowing fine-mapping studies…
PLINK
Desktop

PLINK

A free, open-source whole genome association analysis toolset, designed to…

A free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. The focus of PLINK is purely on…

IMPUTE
Desktop

IMPUTE

A computer program for phasing observed genotypes and imputing missing…

A computer program for phasing observed genotypes and imputing missing genotypes. IMPUTE increases accuracy and combines information across multiple reference panels while remaining computationally…

HRC
Dataset

HRC Haplotype Reference Consortium

Creates a large references panel of human haplotypes by combining together…

Creates a large references panel of human haplotypes by combining together sequencing data from multiple cohorts. HRC is a reference panel of 64 976 human haplotypes at 39 235 157 single nucleotide…

SNPTEST
Desktop

SNPTEST

A program for the analysis of single SNP association in genome-wide studies.…

A program for the analysis of single SNP association in genome-wide studies. The tests implemented include 1) binary (case-control) phenotypes, single and multiple quantitative phenotypes, 2)…

LinkImpute
Desktop

LinkImpute

Performs both genotype calling and imputation. LinkImpute uses sequence read…

Performs both genotype calling and imputation. LinkImpute uses sequence read information. It permits to investigate the effects of missingness and read depth thresholds on the size and accuracy of…

MACH
Desktop

MACH

It can resolve long haplotypes or infer missing genotypes in samples of…

It can resolve long haplotypes or infer missing genotypes in samples of unrelated individuals. Specifically, MACH can estimate haplotypes, impute missing genotypes in a variety of populations, using…

SHAPEIT
Desktop

SHAPEIT Segmented HAPlotype Estimation and Imputation Tool

A method for estimating haplotypes, using genotype data from unrelated samples…

A method for estimating haplotypes, using genotype data from unrelated samples or small nuclear families, that leads to improved accuracy and speed compared to several widely used methods. SHAPEIT…

genipe
Desktop

genipe GENome-wide Imputation PipelinE

A complete genome-wide imputation pipeline which includes automatic reporting,…

A complete genome-wide imputation pipeline which includes automatic reporting, imputed data indexing and management, and a suite of statistical tests for imputed data commonly used in genetic…

Sanger…
Web

Sanger Imputation Service

Provides genotype imputation and phasing service. Sanger Imputation Service is…

Provides genotype imputation and phasing service. Sanger Imputation Service is a web application which allows to upload genome-wide association study (GWAS) data and receive imputed and phased…

Michigan…
Web

Michigan Imputation Server

Provides a genotype imputation service using Minimac3. Michigan Imputation…

Provides a genotype imputation service using Minimac3. Michigan Imputation Server allows to upload phased or unphased genome-wide association study (GWAS) genotypes and receive phased and imputed…

SNP and indel…
Dataset

SNP and indel Imputability

A publicly available SNP and indel imputability database, aiming to provide…

A publicly available SNP and indel imputability database, aiming to provide direct access to imputation accuracy information for markers identified by the 1000 Genomes Project across four major…

FAPI
Desktop

FAPI Fast and Accurate P-value Imputation

A powerful multi-thread Java-based application developed to infer p-values of…

A powerful multi-thread Java-based application developed to infer p-values of untyped Single-nucleotide polymorphisms (SNPs) through p-values of SNPs in LD with the untyped one. With similar…

BIMBAM
Desktop

BIMBAM Bayesian IMputation-Based Association Mapping

A framework for the analysis of association studies. Bim-Bam is designed to…

A framework for the analysis of association studies. Bim-Bam is designed to allow untyped variants to be more effectively and directly tested for association with a phenotype. Compared with standard…

fetalfraction-S…
Desktop

fetalfraction-SNPimpute

Surveys fetal fractions using single nucleotide polymorphism (SNP) imputation.…

Surveys fetal fractions using single nucleotide polymorphism (SNP) imputation. fetalfraction-SNPimpute is able to produce accurate results as well as semiconductor sequencing and low coverage to…

minimac
Desktop

minimac

A lower memory and more computationally efficient implementation of the…

A lower memory and more computationally efficient implementation of the genotype imputation algorithms in minimac and minimac2. Minimac3 is designed to handle very large reference panels in a more…

fastPHASE
Desktop

fastPHASE

A statistical model for patterns of genetic variation in samples of unrelated…

A statistical model for patterns of genetic variation in samples of unrelated individuals from natural populations. fastPHASE is based on the idea that, over short regions, haplotypes in a population…

SNPMStat
Desktop

SNPMStat

A command-line program for the statistical analysis of SNP-disease association…

A command-line program for the statistical analysis of SNP-disease association in case-control/cohort/cross-sectional studies with potentially missing genotype data. SNPMStat allows the user to…

FISH
Desktop

FISH

A method for performing diploid genotype imputation based on the hidden Markov…

A method for performing diploid genotype imputation based on the hidden Markov model. FISH is suitable for large-scale dataset analyses. Both simulation studies and real-data analyses demonstrated…

fcGENE
Desktop

fcGENE

Simplifies and automates the use of different existing analysis packages,…

Simplifies and automates the use of different existing analysis packages, especially during the workflow of genotype imputations and corresponding analyses. fcGENE transforms SNP data and imputation…

ASGSCA
Desktop

ASGSCA

Provides tools to model and test the association between multiple genotypes and…

Provides tools to model and test the association between multiple genotypes and multiple traits, taking into account the prior biological knowledge. ASGSCA is an Association Studies for multiple…

MOLGENIS-impute
Desktop

MOLGENIS-impute

Gives priority to the ease of setting up, configuring and running an…

Gives priority to the ease of setting up, configuring and running an imputation. MOLGENIS-impute is an ‘imputation in a box’ solution that seamlessly and transparently automates the set up and…

1000G Marker…
Web

1000G Marker Imputability

A publicly available SNP and indel imputability database, aiming to provide…

A publicly available SNP and indel imputability database, aiming to provide direct access to imputation accuracy information for markers identified by the 1000 Genomes Project across four major…

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…

SVS
Desktop

SVS SNP and Variation Suite

Allows to perform complex analyses and visualizations on genomic and phenotypic…

Allows to perform complex analyses and visualizations on genomic and phenotypic data. SVS provides a set of tools to (1) empower quickly and easily perform quality-assurance and statistical tests for…

MULTIPOP
Desktop

MULTIPOP

Aids researchers in choosing a successful design. MULTIPOP is a software…

Aids researchers in choosing a successful design. MULTIPOP is a software package which searches for the best combination of populations from a pool of available populations to maximize the…

IGG
Web

IGG

Merges large amount of genotype data and devised functions. IGG aims to…

Merges large amount of genotype data and devised functions. IGG aims to facilitate whole-genome imputation. It integrates HapMap genotypes into local projects by using annotation-guided method. This…

TUNA
Desktop

TUNA Testing UNtyped Alleles

Implements a fast and efficient algorithm for testing association of genotyped…

Implements a fast and efficient algorithm for testing association of genotyped and ungenotyped variants in genome-wide case-control studies. TUNA uses Linkage Disequilibrium (LD) information from…

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