skater

skater performs SNP-based kinship analysis and evaluation in R, providing functions for pedigree import and parsing, genome-wide relationship estimation, relationship degree inference, benchmarking of relationship classification, and IBD (Identity-By-Descent) segment summarization.

Key Features:

• R package implementation: Provides functions and data structures within the R environment for kinship analysis workflows.
• Pedigree import and parsing: Imports, parses, and analyzes pedigree data for downstream relationship estimation.
• Genome-wide relationship estimation: Operates on genome-wide SNP data to estimate pairwise genetic relationships.
• Relationship degree inference: Infers degrees of relatedness between individuals based on SNP-derived metrics.
• Benchmarking capabilities: Supports benchmarking and evaluation of relationship degree classification against known standards or datasets.
• IBD segment summarization: Summarizes IBD (Identity-By-Descent) segments to quantify shared genetic segments between individuals.

Scientific Applications:

• Population genetics: Estimating relatedness and patterns of shared ancestry within and between populations using SNP data.
• Conservation biology: Assessing genetic relatedness for management of breeding programs and monitoring genetic diversity.
• Human genetics: Identifying familial relationships, pedigree verification, and studies of inheritance using genome-wide SNPs and IBD segments.

Methodology:

Performs SNP-based kinship analysis using genome-wide SNP data to estimate relationships and summarize IBD segments.