ngs-dna-somatic-variants
Pass
Audited by Gen Agent Trust Hub on Aug 15, 2026
Risk Level: SAFECOMMAND_EXECUTION
Full Analysis
- Command Execution Pattern: The skill provides instructions for running bioinformatics scripts (ngs_preflight.py and run_dna_somatic_variants.py) located within its local directory structure. These scripts serve as the orchestrators for the variant calling pipeline.
- Data Input Integration: The workflow processes various file formats including sample sheets (TSV), genomic alignments (BAM/CRAM), and reference genomes. This input surface is necessary for performing DNA variant calling tasks.
- Integration with Established Pipelines: Information provided directs the agent to utilize standard industry workflows like GATK Mutect2 and nf-core/sarek, which are well-known and reputable resources in the bioinformatics community.
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