manta

manta detects structural variants (SVs) from next-generation sequencing data, identifying deletions, duplications, inversions, and translocations for germline and somatic variant analysis.

Key Features:

• Robust detection algorithms: Integrates multiple evidence types from next-generation sequencing, including split-reads, paired-end reads, and read-depth, to improve precision and recall in SV detection.
• Supported SV types: Calls deletions, duplications, inversions, and translocations.
• Germline and somatic calling: Supports both germline and somatic structural variant identification.
• Interoperability with Bioconductor: Integrates with Bioconductor packages in R to enable downstream analysis and data exchange.

Scientific Applications:

• Cancer genomics: Identification of somatic structural variants that can drive tumorigenesis and cancer progression.
• Genetic disorders: Detection of germline SVs associated with inherited diseases.
• Evolutionary biology: Analysis of genomic rearrangements across species to study evolutionary processes.

Methodology:

Preprocessing of sequencing reads (quality filtering and alignment to a reference genome), integration of split-read, paired-end, and read-depth evidence to nominate SVs, variant calling to distinguish true positives from false positives, and annotation and filtering of detected variants by quality metrics.