vntyper online frontend

Table of Contents

• Overview
• Features
• Technologies Used
• Usage
• File Naming Conventions
• License

Overview

vntyper-online-frontend is a web-based application designed to facilitate the extraction of specific genomic regions from BAM files using their corresponding BAI index files. Leveraging the power of BioWasm's Aioli, the application runs samtools directly in the browser, enabling users to process their genomic data without the need for backend servers or local installations.

Features

• Single File Input for BAM and BAI Files: Users can upload multiple BAM and BAI files simultaneously through a single file input, streamlining the upload process.
• Predefined Region Selection: A dropdown menu allows users to select predefined genomic regions, reducing the likelihood of input errors.
• In-Browser Processing: Utilizes samtools via BioWasm's Aioli to perform region extraction directly in the browser.
• Download Extracted BAM Files: After processing, users can download the subset BAM files corresponding to their selected regions.
• User-Friendly Interface: Clean and intuitive UI ensures ease of use for both novice and experienced users.
• Error Handling: Provides clear error messages for missing files or processing issues, guiding users to rectify problems.

Technologies Used

• HTML5 & CSS3: For structuring and styling the user interface.
• JavaScript (ES6): Handles file uploads, processing logic, and user interactions.
• BioWasm's Aioli: Enables running samtools in the browser for genomic data processing.
• samtools: A suite of programs for interacting with high-throughput sequencing data.

Running Locally

1. Clone the Repository:

   git clone https://github.com/yourusername/vntyper-online-frontend.git

2. Navigate to the Project Directory:

   cd vntyper-online-frontend

3. Open the Application:

   Open the index.html file in your preferred web browser.

Usage

1. Select BAM and BAI Files:

   • Click on the "Select BAM and BAI Files" button.
   • In the file selection dialog, navigate to the directory containing your BAM and BAI files.
   • Select the desired BAM files along with their corresponding BAI files.
     • Naming Conventions:
       • For a BAM file named sample.bam, the corresponding BAI file should be either sample.bam.bai or sample.bai.
   • Click "Open" to upload the selected files.

2. Select Genomic Region:

   • From the "Select Region" dropdown, choose the desired genomic region.
   • The dropdown defaults to the hg38 MUC1 locus. You can switch to hg19 if needed.

3. Extract Region:

   • Click the "Extract Region" button.
   • The button will display "Processing..." while the extraction is underway.
   • A loading spinner indicates that processing is in progress.

4. Download Extracted BAM Files:

   • Once processing is complete, download links for the subset BAM files will appear under the "output" section.
   • Click on the "Download subset_*.bam" links to download the extracted regions.

5. Verify Downloaded Files:

   • Ensure that the downloaded BAM files are of the expected size and contain the reads from the specified region.

File Naming Conventions

To ensure successful processing, adhere to the following naming conventions for your BAM and BAI files:

• For a BAM file named example.bam, the corresponding BAI file should be either:
  • example.bam.bai
  • example.bai

Example:

example.bam
example.bam.bai

or

example.bam
example.bai

Ensure that each BAM file has its corresponding BAI file following one of the above naming patterns.

License

This project is licensed under the MIT License.

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Acknowledgements

• BioWasm for providing the Aioli library.
• samtools for their powerful genomic data processing tools.
• HTSLIB for maintaining open-source tools for high-throughput sequencing data.