Merlin

Merlin performs likelihood-based analysis of dense single-nucleotide polymorphism (SNP) maps in pedigree data to support linkage, association, haplotyping, and identity-by-descent inference.

Key Features:

• Efficient analysis of dense genetic maps: Handles high-density SNP maps to perform allele-sharing analyses and haplotyping on large marker sets.
• Sparse binary trees for pedigree representation: Uses sparse binary/inheritance trees to represent gene flow parsimoniously, enabling efficient pedigree traversal and exact likelihood calculations for single markers and multiple linked markers.
• Approximate multipoint calculation: Implements an approximate multipoint calculation that disregards the low-probability event of numerous recombinants to accelerate computation on maps with thousands of markers.
• Rapid likelihood inference: Performs rapid likelihood inference using sparse inheritance trees to support haplotyping, genotype error detection, and affected-pair linkage analyses.
• Handling large marker sets: Scales to a greater number of markers than many pedigree analysis packages, making it suitable for high-density SNP studies.
• Error detection and simulation: Provides functions for genotype error detection and simulation to assess and validate analyses.

Scientific Applications:

• Linkage analysis: Supports parametric, non-parametric, and regression-based linkage analyses on pedigree data.
• Association analysis: Conducts association analysis for quantitative traits using high-density SNP data.
• IBD and kinship estimation: Estimates identity-by-descent (IBD) and kinship within pedigrees.
• Error detection and simulation: Detects genotype errors and runs simulations to evaluate analysis robustness.

Methodology:

Uses sparse binary/inheritance trees to represent gene flow and traverse pedigrees, performs exact likelihood calculations for single and multiple linked markers, and applies an approximate multipoint calculation that ignores the low-probability event of numerous recombinants to accelerate inference.