Welcome to auto-acmg

Auto-acmg is a comprehensive software suite designed for the automatic prediction of ACMG (American College of Medical Genetics and Genomics) criteria for the evaluation of sequence variants and copy number variations (CNVs) in genetic data. Its primary function is to assist geneticists and researchers by providing a systematic approach to classify genetic variants according to established guidelines. More information to the guidelines can be found at the ACMG Sequence Variant Criteria and AMCG Sequence Variant Details sections.

Key Features

• Variant Classification: Auto-acmg classifies single nucleotide variants (SNVs) and CNVs based

  on ACMG guidelines, enhancing the accuracy and consistency of genetic interpretations.

• Implementation of ACMG Criteria: It supports a range of criteria including PVS1, PS1, PM1,

  PM2, PM4, PM5, PP2, PP3, BA1, BS1, BS2, BP1, BP3, BP4 and BP7, allowing users to assess the pathogenicity of variants in a comprehensive manner.

• VCEP Specifications: The software is designed to adhere to Variant Curation Expert Panel

  (VCEP) specifications, ensuring that each prediction is tailored to the specific genes and conditions studied by expert panels.

• Extensible and Adaptable: Auto-acmg can be customized and extended to accommodate new criteria

  and guidelines as genetic science evolves.

Getting Started

If you are new to auto-acmg, a good starting point is the Usage section which provides detailed instructions on how to use the software effectively.

If you are interested in contributing to auto-acmg, please refer to the Dev Quickstart section.

Also pay attention to the Auto-ACMG Implementation section to understand how auto-acmg works internally.

Contents:

• Auto-ACMG Implementation
  • Workflow Overview
  • VCEP-Specific Overrides
  • Link to Source Code
• AMCG Sequence Variant Details
  • Data
  • References
  • Criteria
• ACMG Sequence Variant Criteria
  • Mode of Inheritance
  • Allele Frequency
  • Calibration
  • Transcript Selection
  • Pathogenicity Predictions
  • Code Modification Nomenclature
  • Rules / Point System
  • Criteria
• Implementation of different ACMG criteria for sequence variants
  • PVS1
  • PS1 and PM5
  • PM1
  • PM2, BA1, BS1, BS2
  • PM4 and BP3
  • PP2 and BP1
  • PP3 and BP4
  • BP7
• Implementation of different ACMG criteria for structural variants
  • PVS1
• Benchmarking
  • Methodology
  • How to Run the Benchmarking Script
  • Results
  • Conclusion

Usage:

• Usage
  • Building the Docker Image
  • Setting Up Volumes
  • Running the Docker Image
  • Configuring the Environment File
  • Accessing the OpenAPI Documentation
  • API Endpoints

Development:

• Dev Quickstart
  • Overview
  • Prerequisites
  • Clone Rsepository
  • Install Dependencies
  • Set up the SeqRepo
  • Set up the .env file
  • Running the CLI

Internal API Documentation:

• REEV API Reference
  • Annonars
  • Dotty
  • Mehari
• API Endpoints