NVIDIA Parabricks v4.6 Enhances Variant Calling Accuracy

NVIDIA has released Parabricks v4.6, a genomics software suite designed to accelerate secondary analysis for data scientists and bioinformaticians. This update introduces significant improvements in variant calling accuracy by integrating Google’s DeepVariant and DeepSomatic 1.9, including a pangenome-aware mode for enhanced precision across diverse genetic variations and populations.

The new version also features enhancements to STAR, a tool for accelerating RNA-sequencing alignment, and offers nearly 8x faster performance on NVIDIA GPUs compared to CPU-only solutions. These updates make Parabricks v4.6 a powerful tool for genomic research and analysis.

Key Features of Parabricks v4.6

DeepVariant and DeepSomatic 1.9: Incorporates pangenome-aware DeepVariant for improved accuracy.
DeepSomatic Support: Adds support for long-read and whole exome sequencing (WES).
STAR quantMode: Includes GeneCounts for fast generation of gene-level read counts.
STAR Speedups: Achieves nearly 8x faster performance on two NVIDIA RTX PRO 6000 GPUs compared to CPU-only solutions.
Mutectcaller Enhancements: Provides additional arguments, including mitochondrial mode.

Enhanced Variant Calling with DeepVariant

The integration of Giraffe with pangenome-aware DeepVariant in Parabricks v4.6 significantly improves variant identification accuracy and speeds up the analysis process. Tests using four NVIDIA RTX PRO 6000 GPUs demonstrated a reduction in runtime from over 9 hours on CPU-only solutions to under 40 minutes.

Existing Parabricks users can access DeepVariant by providing the FASTA reference file from the Giraffe index files, a BAM file, and the graph GPZ file output from running Giraffe. Detailed instructions are available in the Parabricks Giraffe documentation.

STAR Improvements for RNA-Sequencing

STAR also sees improvements in Parabricks v4.6, with the new quantMode GeneCounts option enabling fast gene-level read counts during the mapping step. This benefits gene expression analysis, QC, normalization, and data integration.

Users can download NVIDIA Parabricks v4.6 to begin using GPU-accelerated genomic analysis. The NVIDIA Parabricks Developer Forum is available for further discussion and support.