Canary

Canary converts paired FASTQ files from amplicon NGS assays into annotated Variant Call Format (VCF) files for clinical variant analysis.

Key Features:

• Single-Program Solution: Performs end-to-end processing from paired FASTQ input to annotated VCF within a single program.
• Comprehensive Variant Processing: Executes quality control, alignment, variant calling, 3' shifting, and parsimonious representation of variants.
• Handling of Complex Variants: Represents proximate in-phase multi-nucleotide polymorphisms (MNPs) as single HGVS "delins" variants.
• Extensive Annotation Capabilities: Annotates variants with attributes from MyVariant.info, including pathogenicity, population statistics, and in‑silico predictors.

Scientific Applications:

• Clinical variant calling from amplicon assays: Converts amplicon NGS data into clinically interpretable variant calls in VCF format.
• Variant normalization for reporting: Produces 3' shifted, most-parsimonious HGVS representations to standardize variant nomenclature.
• Annotation-driven interpretation: Integrates pathogenicity, population frequency, and in‑silico predictor annotations to support clinical interpretation.
• Clinical sequencing workflows: Applied in clinical sequencing at the Peter MacCallum Cancer Centre for processing clinical data.

Methodology:

Accepts paired zipped FASTQ files, performs quality control, alignment, variant calling, 3' shifting and parsimonious normalization of variants, collapses proximate in‑phase variants to HGVS delins for MNPs, and annotates variants using MyVariant.info, producing an annotated VCF.