Research & Analysis
Genomic Sequence Analysis Pipeline
Designs production-grade genomic sequence analysis pipelines for variant discovery, annotation, and clinical interpretation. Implements GATK best practices with custom optimizations for research or clinical applications, supporting WGS, WES, and targeted panel sequencing.
Prompt
--- ## Example Usage ### Input Building clinical WGS pipeline for rare disease diagnosis program. Need to analyze 1000 trios (3000 samples) per year, germline variant calling with focus on SNVs, indels, and CNVs. Must be CLIA-compliant, <7 day turnaround from sample receipt to clinical report. Have AWS infrastructure budget, need to integrate with existing LIMS. Annotation must include ClinVar, OMIM, gnomAD, and internal variant database. ### Output **Clinical WGS Pipeline: Rare Disease Diagnosis** **Compliance Framework: CLIA/CAP Ready** **Pipeline Architecture**