xAtlas

xAtlas calls single-nucleotide variants (SNVs) and small insertions and deletions (indels) from next-generation sequencing (NGS) data to produce variant call sets for downstream genomic analyses.

Key Features:

• Single-sample variant calling: Calls SNVs and small indels from individual NGS samples.
• Rapid processing and accuracy: Reports SNVs with 99.11% recall and 98.43% precision on the HG002 reference at 60× whole-genome coverage in under two CPU hours.
• File format support: Supports CRAM input and gVCF output.
• Retraining capabilities: Includes retraining functionality to adapt the calling model as new data become available.
• Scalability: Processed 3,202 samples at 30× whole-genome coverage from the 1000 Genomes Project with an average runtime of 1.7 hours per sample.
• Population analysis compatibility: Called SNVs enabled clear separation of individual populations in principal component analysis.

Scientific Applications:

• Genomic research: Variant discovery for studies of genetic variation within and between populations.
• Disease genomics: Identification of variants associated with diseases for genetic association and pathology studies.
• Personalized medicine: Generation of individual-level variant call sets to support precision medicine analyses.

Methodology:

Performs single-sample variant calling of SNVs and small indels from heterogeneous NGS data, supports CRAM input and gVCF output, and includes retraining of its calling model.