Psi-Caller: A Lightweight Short Read-Based Variant Caller With High Speed and Accuracy

Area of Science:

• Genomics
• Bioinformatics
• Computational Biology

Background:

• Population-scale resequencing studies are crucial for understanding human genome variants and phenotypes.
• Variant calling is a core bioinformatics task in genomics, but current tools are computationally intensive.
• Genomics research demands higher yields and efficiency in variant calling.

Purpose of the Study:

• To develop a lightweight variant calling algorithm that achieves both high performance and yield.
• To introduce Psi-caller, an efficient tool for single nucleotide polymorphism (SNV) and Indel calling from short-read sequencing data.

Main Methods:

• Categorizing candidate variant sites based on complexity and location.
• Employing binomial models, partial-order alignment, and de Bruijn graph-based local assembly.
• Developing Psi-caller, a novel algorithm for SNV and Indel genotyping.

Main Results:

• Psi-caller demonstrates significantly faster performance compared to state-of-the-art tools.
• The algorithm achieves higher or equal sensitivity and accuracy in variant calling.
• Benchmarks on simulated and real data confirm Psi-caller's efficiency and reliability.

Conclusions:

• Psi-caller is a computationally efficient and accurate variant caller for short-read sequencing data.
• The tool's performance and yield make it suitable for large-scale genomics studies.
• Psi-caller has the potential to advance population-scale genetic variation studies.