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IBD segment detection software tools | Genome-wide association analysis

Recently, investigators have proposed state-of-the-art Identity-by-descent (IBD) mapping methods to detect IBD segments between purportedly unrelated individuals. The IBD information can then be used for association testing in genetic association…
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…

SNPRelate
Desktop

SNPRelate

Offers a way to solve large-scale, numerically intensive genome wide…

Offers a way to solve large-scale, numerically intensive genome wide association studies (GWAS) calculations on multi-core symmetric multiprocessing computer architectures. SNPRelate permits basic…

GERMLINE
Desktop

GERMLINE

An algorithm for discovering long shared segments of Identity by Descent (IBD)…

An algorithm for discovering long shared segments of Identity by Descent (IBD) between pairs of individuals in a large population. GERMLINE takes as input genotype or haplotype marker data for…

BEAGLE…
Desktop

BEAGLE (fastIBD)

Performs genotype calling, genotype phasing, imputation of ungenotyped markers,…

Performs genotype calling, genotype phasing, imputation of ungenotyped markers, and identity-by-descent segment detection. FastIBD can be applied to thousands of samples across genome-wide SNP data…

HaploShare
Desktop

HaploShare

Detects extended haplotypes that are shared by multiple individuals, and allows…

Detects extended haplotypes that are shared by multiple individuals, and allows comparisons between cases and controls. Testing on simulated and real cases demonstrated significant improvements in…

HapFABIA
Desktop

HapFABIA

A method for identifying very short IBD segments that are tagged by rare…

A method for identifying very short IBD segments that are tagged by rare variants in large sequencing data. In artificial and simulated data, HapFABIA outperformed IBD detection methods such as…

GraphIBD
Desktop

GraphIBD

A free, open-source IBD association testing software for genome-wide…

A free, open-source IBD association testing software for genome-wide association study analysis. GraphIBD requires an IBD detection method such as Beagle FastIBD to run first. Then GraphIBD builds…

EMI
Desktop

EMI Efficient Multiple-IBD

A clustering method, efficient multiple-IBD, which uses pairwise IBD segments…

A clustering method, efficient multiple-IBD, which uses pairwise IBD segments to infer multiple-haplotype IBD clusters. It expands clusters from seed haplotypes by adding qualified neighbors and…

DASH
Desktop

DASH DASH Associates Shared Haplotypes

A software tool that builds upon pairwise IBD shared segments to infer clusters…

A software tool that builds upon pairwise IBD shared segments to infer clusters of IBD individuals. Briefly, for each locus, DASH constructs a graph with links based on IBD at that locus, and uses an…

CrypticIBDcheck
Desktop

CrypticIBDcheck

An R package to identify pairs of closely-related subjects based on genetic…

An R package to identify pairs of closely-related subjects based on genetic marker data from single-nucleotide polymorphisms (SNPs). The package is able to accommodate SNPs in linkage disequibrium…

IBD-Groupon
Desktop

IBD-Groupon

A method to detect group-wise IBD tracts based on pairwise IBD relationships.…

A method to detect group-wise IBD tracts based on pairwise IBD relationships. This method does not need to specify the number of IBD groups, which will be detected automatically. IBD-Groupon takes LD…

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