Identity by descent identification software tools | Population genetics data analysis
Two haplotypes are identical by descent if they share the same alleles inherited from a common ancestor. Identity by descent (IBD) can be considered on various timescales. Emerging applications for the detected IBD segments include IBD mapping, haplotype phase inference, genotype imputation, and inference of population structure. Most IBD detection methods are based on hidden Markov models (HMMs) in which, at each DNA locus, a hidden state indicates presence or absence of IBD.
Detects IBD segments and estimates their endpoints using an algorithm that is fast enough to be deployed on the very large whole-genome SNP datasets. We compared the performance of FISHR to three leading IBD segment detection programs: GERMLINE, refinedIBD, and HaploScore. Using simulated and real genomic sequence data, we show that FISHR is slightly more accurate than all programs at detecting long (greater than 3 cM) IBD segments but slightly less accurate than refinedIBD at detecting short (1 cM) IBD segments. Moreover, FISHR outperforms all programs in determining the true endpoints of IBD segments, which is important for several reasons. FISHR takes two to four times longer than GERMLINE to run, whereas both GERMLINE and FISHR were orders of magnitude faster than refinedIBD and HaploScore. Overall, FISHR provides accurate IBD detection in unrelated individuals and is computationally efficient enough to be utilized on large SNP datasets greater than 20,000 individuals.
Allows breeders and researchers to monitor changes in the genetic variability and structure of the populations with limited cost of preparing datasets. ENDOG provides a number of features that may be interest to teachers and students to develop an in-depth understanding of important statistical concepts and procedures for population genetic analysis. It enables to handle very large data files and is particularly designed to the analysis of diploid populations in which no selfing is possible.
Allows detection of genomic regions identical by decent (IBD) for pairs of haploid samples. hmmIBD uses simulated data, benchmarks it against a previously published method for detecting IBD within populations. This tool is conceived to infer IBD segments shared between pairs of haploid genomes and to estimate two quantities: (1) the marginal posterior probability of the IBD state; and (2) the rate at which the genomes transition between states.
A software tool for estimating pairwise relatedness from NGS data. NgsRelate provides maximum likelihood estimates that are based on genotype likelihoods instead of genotypes and thereby takes the inherent uncertainty of the genotypes into account. Using both simulated and real data we show that NgsRelate provides markedly better estimates for low-depth NGS data than two state-of-the-art genotype based methods.
Assists in modeling the transmission of the haplotypes from the closest genotyped relatives along an entire chromosome. CHROMIBD is a method that estimates Identity-by-Descent probabilities (IBDp) to the truly inherited parental chromosome. It is based on a hidden Markov model where hidden states correspond to the set of all possible origins of a haplotype within a given pedigree.