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bio-clinical-databases-hla-typing
Maintainer FreedomIntelligence · Last updated April 1, 2026
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.
Original source
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-clinical-databases-hla-typing
- Maintainer
- FreedomIntelligence
- License
- MIT
- Last updated
- April 1, 2026
Skill Snapshot
Key Details From SKILL.md
Key Notes
- CLI: OptiType for HLA class I typing from DNA/RNA reads.
- CLI: arcasHLA extract → arcasHLA genotype for RNA-seq based 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.
- samtools view -h input.bam chr6:28000000-34000000 | \ samtools fastq -1 hla_R1.fq -2 hla_R2.fq -.
Source Doc
Excerpt From SKILL.md
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.
Run OptiType
OptiTypePipeline.py
-i hla_R1.fq hla_R2.fq
-d
-o optitype_output
-c config.ini
RNA mode
OptiTypePipeline.py
-i rna_R1.fq rna_R2.fq
-r
-o optitype_rna_output
-c config.ini
Use cases
- Use when determining HLA genotype for transplant matching, neoantigen prediction, or pharmacogenomic screening.
Not for
- Do not rely on this catalog entry alone for installation or maintenance details.
Upstream Related Skills
- clinical-databases/pharmacogenomics - HLA-drug interactions
- variant-calling/clinical-interpretation - Clinical reporting
- single-cell/cell-type-annotation - HLA expression
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