Abstract LB160: SMURFS: A comprehensive Nextflow pipeline for consensus somatic variant detection

Key Points

• The central aim is to develop a comprehensive pipeline for accurate somatic variant detection in cancer genomics.
• Developed the SMURFS pipeline using Nextflow for efficient variant calling and quality control.
• Implemented ensemble calling with four algorithms: Mutect2, SAGE, Strelka2, and MuSE2 for consensus detection.
• Incorporated additional tools for copy number and structural variant analysis, enhancing overall somatic variant characterization.
• Supported various input formats and reference genomes, facilitating flexible analyses.
• Achieved significant reduction in false positive rates while maintaining sensitivity for true somatic variants.
• Demonstrated a runtime of 277.8 minutes per sample pair with an operational cost of 17.33 on AWS.
• Validated the pipeline's effectiveness using TCGA whole-exome sequencing samples, confirming its practical applicability.

Abstract