Platform & pipeline — how it actually works.
ℹ️ Note: ATGC Flow is designed to support research and clinical workflows. Variant interpretations generated by automated tools should always be reviewed by a qualified geneticist or genetic counselor before being used to guide clinical decisions.
Platform Overview
ATGC Flow is a whole exome sequencing analysis platform that integrates industry-standard bioinformatics methodology within an automated pipeline to process paired-end FASTQ files through alignment, variant calling, and comprehensive annotation. The platform is designed for research use, with automated ACMG/AMP 2015 variant classification to support — not replace — expert review.
New to WES analysis? Our Genomics Knowledge Base covers the concepts behind every stage of this pipeline, and the Publications & References page lists the peer-reviewed methodology each stage is built on.
Technical Approach
Automated Pipeline
Scalable workflow management for reproducible bioinformatics analysis with automatic parallelization and resource optimization.
Multi-Step Processing
Quality control → alignment → base quality recalibration → variant calling → multi-source annotation.
Comprehensive Annotation
Variant effect prediction, functional annotation, population frequency data, and functional pathogenicity prediction scores.
ACMG Classification
Automated variant classification following ACMG/AMP 2015 guidelines with evidence-based scoring and clinical interpretation support.
Reference Genome & Databases
Reference Genome: GRCh38/hg38 (Genome Reference Consortium Human Build 38)
Known Variants: Curated known-indel reference sets used for base quality recalibration
Annotation Databases: Population frequency, functional prediction, and clinical significance knowledge bases
Gene Panels: Curated disease gene panel sources, ACMG SF v3.2 secondary findings genes
Pipeline Specifications
Input Requirements
- • Paired-end FASTQ files (.fastq.gz)
- • Whole exome sequencing data
- • Minimum 50x mean coverage recommended
- • Illumina platform supported
Output Files
- • BAM file with BQSR (indexed)
- • Raw VCF (gzipped & indexed)
- • Fully annotated VCF
- • Filtered TSV with functional annotations
Limitations & Considerations
Current Limitations
- • Automated ACMG classifications require expert review before clinical reporting
- • Optimized for Illumina paired-end WES data; WGS and targeted panels require configuration adjustments
- • Structural variant detection is under active development
- • Requires bioinformatics expertise for advanced result interpretation
- • Processing time varies with compute resources and sample coverage depth
Future Enhancements
- • Clinical validation studies
- • Enhanced variant filtering options
- • Structural variant detection
- • Pharmacogenomics annotations
- • Export to standard formats (HGVS, VCF 4.3)
- • Batch processing for cohort analysis