variant-calling
Pass
Audited by Gen Agent Trust Hub on Jul 9, 2026
Risk Level: SAFECOMMAND_EXECUTION
Full Analysis
- [SAFE]: The skill implements a legitimate genomic analysis workflow using industry-standard tools like GATK, BWA-MEM2, and SAMtools. The instructions provided in SKILL.md align with GATK best practices for germline and somatic variant calling.
- [COMMAND_EXECUTION]: The provided bash script (
run_germline_pipeline.sh) orchestrates multiple external command-line tools. It utilizes environment variables and positional arguments to configure execution parameters (e.g., thread count, memory allocation). While these parameters are used in shell commands, they are typical for bioinformatics workflows and originate from the user environment. - [SAFE]: The Python script (
filter_by_acmg.py) performs structured data processing on VCF files and JSON configuration. It uses the standardpysamlibrary for genomic file access and does not perform any network operations or dynamic code evaluation.
Audit Metadata