GenomeChronicler

GenomeChronicler detects germline and somatic variants from whole-genome, whole-exome, and targeted sequencing data and annotates them with ancestry, phenotype associations, and population-frequency information for research reporting.

Key Features:

• Variant detection: Processes whole-genome, whole-exome, and targeted sequencing data to identify germline and somatic variants and produce variant statistics.
• Comprehensive annotation and reporting: Generates genome reports that include ancestry, known phenotypic trait associations, genotype prevalence among PGP participants, and population frequency metrics.
• Database integration: Correlates detected genotypes with entries from SNPedia, ClinVar, GETevidence, and gnomAD for annotation and frequency information.
• Clinical curation status: Flags potentially beneficial and potentially harmful variants in reports without providing clinical curation.
• Privacy-focused execution: Supports self-contained offline execution without internet access to enable analysis in secure environments.
• Scalable deployment: Supports parallel processing via the Nextflow workflow manager and distribution as Singularity containers and Docker recipes.

Scientific Applications:

• Genotype–phenotype research: Facilitates research on associations between genetic variants and phenotypic traits by linking genotypes to curated databases.
• Population genetics and prevalence studies: Enables analysis of variant population frequencies and genotype prevalence across PGP participants and reference datasets.
• Individual and cohort-level variant reporting: Produces structured variant reports for research use at individual-sample and high-throughput cohort scales.

Methodology:

Detects variants from whole-genome, whole-exome, and targeted sequencing data; annotates genotypes by querying SNPedia, ClinVar, GETevidence, and gnomAD; supports parallel execution with Nextflow and containerized deployment via Singularity and Docker; can operate offline and generates genome reports with ancestry, phenotype associations, and variant statistics without clinical curation.