octopus

octopus performs haplotype-aware variant calling to phase and genotype single nucleotide variants, indels, microinversions, and small complex replacements across germline and somatic contexts and across varying ploidy levels.

Key Features:

• Unified haplotype-aware framework: Integrates sequencing reads and prior information within a single framework that accommodates different experimental designs and ploidy levels.
• Polymorphic Bayesian genotyping model: Uses a Bayesian genotyping model to call and phase genotypes in both germline and somatic contexts.
• Dynamic haplotype tree construction: Constructs and manages a tree of haplotypes that is dynamically pruned and extended based on posterior probabilities using particle-filter-like techniques.
• Low-frequency somatic variant detection: Detects low-frequency somatic variations with sensitivity to rare mutations while controlling false positive rate.
• Supported variant types: Calls single nucleotide variants, indels, and small complex replacements such as microinversions.
• Realigned evidence output: Produces realigned evidence BAM files for validation and interpretation of variant calls.

Scientific Applications:

• Germline variant calling: Accurate calling of SNVs, indels, microinversions, and small complex replacements in germline samples.
• Somatic mutation detection: Identification of low-frequency somatic variants relevant to cancer genomics and studies of mosaicism.
• Phasing and genotyping across ploidy levels: Phasing and genotype inference in diploid and non-diploid organisms and across diverse experimental designs.

Methodology:

Constructs and manages a dynamic haplotype tree that is pruned and extended based on posterior probabilities using particle-filter-like techniques; integrates sequencing reads and prior information within a polymorphic Bayesian genotyping model to phase and call genotypes; outputs realigned evidence BAM files.