Manta

Manta detects structural variants (SVs) and indels from next-generation sequencing (NGS) data, providing rapid germline and somatic variant calling for downstream genomic analyses.

Key Features:

• Speed and Efficiency: Processes high-coverage human genomes rapidly on standard compute hardware (e.g., NA12878 at 50× genomic coverage in under 20 minutes).
• Comprehensive Variant Detection: Detects structural variants, medium-sized indels, and large insertions using paired-end and split-read evidence.
• Optimized Scoring Models: Implements scoring models tailored for diploid germline analysis and somatic tumor–normal pairs, with call quality assessed by pedigree-consistency checks and comparisons to COSMIC variants.
• High-Resolution Assembly: Performs local assembly to resolve a higher fraction of variant breakpoints to base-pair resolution to aid downstream annotation and clinical interpretation.

Scientific Applications:

• Genomic Research: Enables comprehensive analysis of genetic variation for studies of disease genetics and evolutionary biology.
• Clinical Genomics: Supports structural variant and indel detection in clinical genomic analyses to identify clinically significant variants.
• Cancer Genomics: Enables somatic mutation and structural variant detection in tumor–normal sample pairs for cancer research and targeted therapy investigations.

Methodology:

Uses paired-end and split-read evidence, local assembly to base-pair resolution, and specialized scoring models for diploid germline and somatic tumor–normal analyses; validation methods include pedigree-consistency checks and comparisons to COSMIC.