TrioCaller

TrioCaller performs LD-aware genotype calling and phasing by integrating linkage disequilibrium and familial transmission information to improve genotype inference in family-based sequencing studies.

Key Features:

• LD-aware genotype calling: Utilizes linkage disequilibrium (LD) patterns to improve genotype inference, particularly for low to modest coverage sequence data.
• Familial transmission integration: Incorporates familial transmission patterns to enhance phasing and genotype calling in nuclear and multi-generational family structures beyond simple parent-offspring trios.
• External reference panel support: Incorporates external reference panels to increase genotype call accuracy when sample sizes are limited.
• Simulation-based validation: Demonstrated in simulation studies to improve genotype calling accuracy and reduce phasing and Mendelian errors at low to modest coverage.
• Empirical performance on WGS cohort: Shown to outperform methods that do not use family constraints or LD on a whole genome sequencing dataset of 1,339 individuals from the Minnesota Center for Twin and Family Research.

Scientific Applications:

• Family-based sequencing projects: Applicable to analyses of complex familial datasets requiring accurate genotype calling and phasing.
• Variant discovery and genetic research: Supports detection and study of common and rare genetic variants in human genetics research.

Methodology:

Integrates linkage disequilibrium patterns with familial transmission information and can incorporate external reference panels for LD-aware genotype calling and phasing.