Fast and accurate DNASeq variant calling workflow composed of LUSH toolkit

Area of Science:

• Genomics
• Bioinformatics
• Computational Biology

Background:

• Whole genome sequencing (WGS) is crucial for molecular diagnosis, staging, and prognosis.
• Current variant calling pipelines like GATK face limitations in computational speed and efficiency for large-scale WGS data.
• The increasing prevalence of WGS necessitates faster and more efficient analysis tools.

Purpose of the Study:

• To introduce and evaluate a novel, fast, and accurate DNASeq variant calling workflow using the LUSH toolkit.
• To compare the performance of the LUSH pipeline against the established GATK pipeline for WGS data analysis.
• To assess the potential of the LUSH pipeline for various genomic applications.

Main Methods:

• Development of a variant calling workflow exclusively using tools from the LUSH toolkit.
• Performance evaluation using the NA12878 dataset at 30x coverage.
• Comparison of precision, recall, and processing speed against the GATK pipeline.

Main Results:

• The LUSH pipeline demonstrated high consistency with GATK, achieving precision and recall rates exceeding 99%.
• The LUSH pipeline completed 30x WGS data analysis in 1.6 hours, approximately 17 times faster than GATK.
• The LUSH_HC tool processed BAM to VCF in 12 minutes, about 76 times faster than GATK.

Conclusions:

• The LUSH pipeline presents a highly promising, faster alternative to GATK for WGS data analysis.
• This accelerated variant calling has significant potential for bedside analysis, large cohort studies, and crop breeding.
• The LUSH pipeline's scalability and deployability make it suitable for diverse clinical and research settings.