Indentify by descent segment detection software tools | Genome-wide association study data 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 studies.
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 analysis of genotype/phenotype data, so there is no support for steps prior to this (e.g. study design and planning, generating genotype or CNV calls from raw data). Through integration with gPLINK and Haploview, there is some support for the subsequent visualization, annotation and storage of results.
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 individuals (as well as an optional known pedigree) and generates a list of all pairwise segmental sharing. GERMLINE uses a novel hashing & extension algorithm which allows for segment identification in haplotype data in time proportional to the number of individuals.
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 detection power and reduction of false positive rate by HaploShare relative to other programs.
Identifies very short identity by descent (IBD) segments that are tagged by rare variants in large sequencing data. HapFABIA works in 3 steps: (i) it applies factor analysis for bicluster acquisition (FABIA) biclustering to phased or unphased genotype data, (ii) it extracts IBD segments from FABIA models by distinguishing IBD from identical by state (IBS) without IBD, and (iii) it cuts single nucleotide variants (SNVs) with false correlation from the extracted IBD segments and joins segments.
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 iterative min-cut approach to identify clusters. These are densely connected components, each sharing a haplotype. As DASH slides the local window along the genome, links representing new shared segments are added and old ones expire; these changes cause the resultant connected components to grow and shrink.
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 calculations of sample and single nucleotide polymorphism (SNP) eigenvectors. It allows principal component analysis (PCA) and identity-by-descent (IBD) relatedness analysis on genomic data structure (GDS) genotype files. The tool permits to accelerate computations on SNP data.
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 into consideration, as it is based on pairwise IBD tracts where LD can be easily incorporated.
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 upon the IBD information to test if the IBD segments show association to the traits. This can be a powerful strategy to detect rare variant associations.
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 extends clusters across sliding windows in the genome.
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 (LD), without the need to thin the markers so that they are approximately independent in the population. Sample pairs are identified by superposing their estimated identity-by-descent (IBD) coefficients on plots of IBD coefficients for pairs of simulated subjects from one of several common close relationships.
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