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MubasherMohammed
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hla-typing

Automate HLA allele typing from WGS/WES VCF data into markdown and JSON reports.

Updated May 10, 2026
Search Tags:#bioinformatics#genomics#hla typing#vcf analysis#allele detection
One-click install
npx skills add https://github.com/MubasherMohammed/opencode-BioInfo --skill hla-typing
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: hla-typing
Source: https://github.com/MubasherMohammed/opencode-BioInfo/tree/main/python/skills/hla-typing
Command: npx skills add https://github.com/MubasherMohammed/opencode-BioInfo --skill hla-typing

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires pandas, and includes scripts (resource) components.

What problem does it solve?

This Skill automates the process of HLA allele typing from WGS/WES VCF data, simplifying complex genomics analysis tasks.

Core Features & Use Cases

  • Automated HLA Typing: Process WGS/WES VCF data to determine HLA alleles.
  • Input Validation and Parsing: Validates and parses input files with format detection.
  • Analysis and Reporting: Generates structured markdown reports and machine-readable JSON results.
  • Use Case: Streamline your workflow by automating the extraction and analysis of HLA data from large-scale genomic studies.

Quick Start

Run the hla-typing skill with the input file 'my_data.vcf'.

Frequently Asked Questions about hla-typing

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I automate HLA allele typing from WGS or WES VCF data?▼

You can automate HLA allele typing from WGS or WES VCF data by running this Skill with your input file to parse variants and generate structured markdown reports alongside machine-readable JSON results.

What is HLA typing and how does VCF analysis fit into the workflow?▼

HLA typing identifies specific human leukocyte antigen alleles from genomic sequences. VCF analysis provides the variant calls from WGS or WES data required to detect these alleles and generate structured typing reports.

Do I need pandas to run HLA allele detection on VCF files?▼

Yes, you need pandas installed as it is required for data manipulation during HLA allele detection from VCF files. The Skill is compatible with macOS and Linux environments.

Can I use this HLA typing process on macOS and Linux systems?▼

Yes, this HLA typing process is compatible with both macOS and Linux systems. You simply need a valid VCF input file and the pandas dependency installed to run the analysis.

What output formats are generated when extracting HLA data from VCF files?▼

Extracting HLA data from VCF files generates structured markdown reports for human review and machine-readable JSON results containing the detected allele data for downstream analysis.

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