GLnexus

GLnexus enables scalable joint variant calling for large cohort sequencing projects by combining joint calling algorithms with a persistent database.

Key Features:

• Scalable Joint Calling: Algorithms scale to the largest foreseeable human cohorts, demonstrated on 50,000 exomes with comparable or better results than existing methods at a fraction of computational cost.
• Persistent Database: Database grows efficiently as additional participants are sequenced without requiring complete reprocessing.
• gVCF Merging: Merges gVCF files as a core operation for population-scale variant calling.
• Cloud Deployment: Available as a standalone open-source version and a DNAnexus cloud-native deployment supporting very large projects.

Scientific Applications:

• Population Genomics: Joint variant calling for cohorts exceeding 240,000 exomes and 22,000 whole-genomes to support genotype/phenotype association studies.
• Exome Sequencing: Validated on 50,000 exomes for complete and accurate genotype generation from large raw datasets.
• Whole-Genome Sequencing: Applied to cohorts of over 22,000 whole-genomes for comprehensive variant detection.

Methodology:

GLnexus combines scalable joint calling algorithms with a persistent database; validation was performed using 50,000 exomes compared against existing methods.