bio-clinical-databases-hla-typing
Call HLA alleles from NGS data using OptiType, HLA-HD, or arcasHLA for immunogenomics applications. Use when determining HLA genotype for transplant matching, neoantigen prediction, or pharmacogenomic screening.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-clinical-databases-hla-typing --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## Version Compatibility Reference examples tested with: OptiType 1.3+, STAR 2.7.11+, pandas 2.2+, samtools 1.19+ Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures - CLI: `<tool> --version` then `<tool> --help` to confirm flags If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # HLA Typing **"Determine HLA genotype from my sequencing data"** → Call HLA alleles from WGS/WES/RNA-seq reads for transplant matching, neoantigen prediction, or pharmacogenomic screening. - CLI: `OptiType` for HLA class I typing from DNA/RNA reads - CLI: `arcasHLA extract` → `arcasHLA genotype` for RNA-seq based typing ## OptiType (HLA Class I) **Goal:** Call HLA Class I alleles (HLA-A, B, C) at 4-field resolution from WGS, WES, or RNA-seq data. **Approach:** Extract HLA region reads from BAM, then run OptiType's integer linear programming algorithm to determine optimal allele assignment. ### From DNA-seq ```bash # Extract HLA reads from BAM samtools view -h input.bam chr6:28000000-34000000
- Version Compatibility
- OptiType (HLA Class I)
- From DNA-seq
- From RNA-seq
- OptiType Config
- HLA-HD (Full Resolution)
- arcasHLA (RNA-seq)
- arcasHLA Merge
- HLA Nomenclature
- HLA and Pharmacogenomics
- Parse OptiType Results
- Class I vs Class II
- Tool Comparison
- Related Skills
Extract HLA reads from BAM samtools view -h input.bam chr6:28000000-34000000 | \ samtools fastq -1 hla_R1.fq -2 hla_R2.fq - Run OptiType OptiTypePipeline.py \ Contains HLA-A, HLA-B, HLA-C alleles (4-field resolution) RNA mode HLA-HD for high-resolution typing Supports Class I and Class II Extract HLA reads
What does the bio-clinical-databases-hla-typing skill do?
Call HLA alleles from NGS data using OptiType, HLA-HD, or arcasHLA for immunogenomics applications. Use when determining HLA genotype for transplant matching, neoantigen prediction, or pharmacogenomic screening.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-clinical-databases-hla-typing --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From FreedomIntelligence/OpenClaw-Medical-Skills, a repository with 2,909 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.