batch

Process multiple genetic variants for ACMG/AMP classification with validation and summary generation.

2|1|Updated Apr 11, 2025

Search Tags:#bioinformatics #batch processing #variant classification #acmg/amp #genetic analysis #clinical genomics

Ready to run

npx skills add https://github.com/yi-john-huang/acmg-amp-classifier-mcp --skill batch

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: batch
Source: https://github.com/yi-john-huang/acmg-amp-classifier-mcp/tree/main/.claude/skills/batch
Command: npx skills add https://github.com/yi-john-huang/acmg-amp-classifier-mcp --skill batch

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes scripts (resource) and references (resource) components.

What problem does it solve?

This Skill streamlines the process of classifying multiple genetic variants according to ACMG/AMP guidelines, providing a consolidated summary of results and handling validation and error reporting.

Core Features & Use Cases

Batch Processing: Classify numerous variants in a single request, saving time and effort.
Input Flexibility: Accepts variants via comma-separated or newline-separated lists, or from a file.
Validation & Error Handling: Validates all variants before processing and provides detailed error summaries for failed classifications.
Use Case: A researcher needs to classify 50 variants identified in a new sequencing run. They can submit all 50 variants at once using this Skill and receive a comprehensive report.

Quick Start

Use the batch skill to classify the following variants: NM_000492.3:c.1521_1523delCTT, BRCA1:c.5266dupC, TP53:p.R273H.

Frequently Asked Questions about batch

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

FAQPage Schema

How do I classify multiple genetic variants according to ACMG/AMP guidelines?▼

To classify multiple genetic variants for ACMG/AMP classification, you can submit them as a comma-separated or newline-separated list. The tool processes each variant, generates progress tracking, and returns a consolidated summary report.

What input formats are accepted for batch processing genetic variants?▼

Batch processing genetic variants accepts inputs via comma-separated lists, newline-separated lists, or directly from a file. This input flexibility allows you to submit numerous variants in a single request for efficient classification.

How does batch variant classification handle invalid HGVS notation or errors?▼

Batch variant classification handles errors by validating all inputs before processing using the validate_hgvs tool. It then provides detailed error summaries for any variants that fail classification, ensuring accurate clinical genomics reporting.

Can I export ACMG/AMP variant classification results to CSV or JSON?▼

Yes, you can export ACMG/AMP variant classification results to CSV or JSON formats. The batch processing tool supports various output formats including summary tables, detailed reports, JSON, and CSV for downstream genetic analysis.

What is the best way to analyze 50 variants from a new sequencing run?▼

The best way to analyze 50 variants from a new sequencing run is using batch classification, which accepts all variants at once. It orchestrates validation and classification for each input, returning a comprehensive report of the results.

Are there limitations when submitting numerous variants for clinical genomics batch processing?▼

When submitting numerous variants for clinical genomics batch processing, the main limitation is that all variants must pass initial HGVS validation. Any variants failing this validation step are excluded and detailed in the generated error summary.