VBT

VBT implements approximate 3-way variant matching to improve detection of Mendelian violations in family trios.

Key Features:

• 3-Way Variant Matching: Approximately solves the 3-way variant matching problem to resolve differences in variant representation among trio members.
• Aligner and Variant Calling Benchmarking: Provides benchmarking capabilities for aligners and variant callers using trio concordance metrics.
• vcfeval-based Comparison: Utilizes vcfeval as the core library for variant comparison.
• VCF and FASTA I/O: Leverages htslib to read and write VCF and FASTA files.
• Implementation: Implemented in C++ for computational performance.
• Accuracy Validation: Demonstrated superior accuracy in Mendelian-violation detection compared with previous trio comparison methods.

Scientific Applications:

• Mendelian-violation detection: Precise identification of Mendelian violations in family trio sequencing data.
• Genetic diagnostics: Support for clinical and research workflows that require reliable trio-based variant assessment.
• Population genetics: Evaluation of trio concordance to inform population-level variant analyses.
• Evolutionary biology research: Analysis of inheritance patterns and variant transmission in familial datasets.

Methodology:

Approximately solves the 3-way variant matching problem; performs variant comparison using vcfeval; reads and writes VCF and FASTA via htslib; implemented in C++.