PRIMUS
PRIMUS is a software tool that uses genome-wide estimates of pairwise identity by descent to identify families and quickly reconstruct and score all possible pedigrees that fit the genetic data by using up to third-degree relatives
PRIMUS uses global IBD sharing proportions between pairs of individuals in a family network to iteratively build a pedigree
Padre
Pedigree-Aware Distant-Relationship Estimation (PADRE) combines relationship likelihoods generated by estimation of recent shared ancestry (ERSA) with likelihoods from family networks reconstructed by PRIMUS, improving the power to detect distant relationships between pedigrees. By leveraging pedigree information, PADRE can even identify genealogical relationships between individuals who are genetically unrelated. PADRE greatly expands the range of relationships that can be estimated by using genetic data in pedigrees.
Pedigree Structure Used to Simulate Ninth-Degree Pedigrees
IMMerge
Genomic data are often processed in batches and analyzed together to save time. However, it is challenging to combine multiple large VCFs and properly handle imputation quality and missing variants due to the limitations of available tools. To address these concerns, we developed IMMerge, a Python-based tool that takes advantage of multiprocessing to reduce running time. For the first time in a publicly available tool, imputation quality scores are correctly combined with Fisher's z transformation.
Overview of IMMerge implementation and performance comparison with bcftools on a testing dataset
Drive
Distant Relatedness for Identification and Variant Evaluation (DRIVE) is a novel approach to IBD-based genotype inference used to identify shared chromosomal segments in dense genetic arrays. DRIVE implemented a random walk algorithm that identifies clusters of individuals who pairwise share an IBD segment overlapping a locus of interest.
The DRIVE tool for local IBD clustering.
Other Tools
Our GitHub contains the latest published versions of a variety of other tools