bio-workflows-neoantigen-pipeline
Orchestrates neoantigen discovery from somatic variants to ranked vaccine candidates, chaining HLA typing (OptiType/arc…
Description
Orchestrates neoantigen discovery from somatic variants to ranked vaccine candidates, chaining HLA typing (OptiType/arcasHLA + LOHHLA), VEP annotation (Wildtype+Frameshift plugins) + expression/readcount annotation, proximal-variant phasing, pVACseq MHC-I/II binding, CCF/clonality, and immunogenicity/quality ranking. Use when recognizing that binding is single-digit PPV and the critical steps are downstream (full-resolution HLA + LOH gating, proximal-variant phasing, clonality from purity+CN not raw VAF, expression), sequencing normalize+annotate -> phase -> HLA -> binding -> quality in the defensible order, dropping candidates on LOH-lost alleles, supplying --phased-proximal-variants-vcf so the mutant peptide is real, or ranking WITHIN patient rather than a fixed IC50 threshold. Hands mechanism to the immunoinformatics component skills; not a re-teach of any single step. A reusable SKILL.md agent skill by GPTomics.
Author
GPTomics
Platform
cli
Pricing model
free
Categories
Tags
Capabilities
- 1,053 stars
- SKILL.md package