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AlleleExpress

AlleleExpress is a fast C++ utility for calculating allele frequencies from BAM files at specified genomic positions. It efficiently processes sequencing data to identify variants and quantify their respective allele frequencies.

Features

• Fast processing of BAM files at target positions specified in BED files
• Accurate allele frequency calculation with customizable quality thresholds
• Output in a simple tab-delimited format for easy downstream analysis

Requirements

• C++23 compatible compiler (GCC 13+ or Clang 15+)
• CMake 3.14 or higher
• HTSlib 1.9 or higher

Installation

From Source

1. Clone the repository:

git clone https://github.com/username/allele-express.git
cd allele-express

2. Create a build directory and compile:

cmake -S . -B build
cmake --build build

3. Install (optional):

# Default system-wide installation (requires sudo)
sudo cmake --install build

Custom Installation Location

If you want to install to a custom location, you can specify the CMAKE_INSTALL_PREFIX option:

cmake -S . -B build -DCMAKE_INSTALL_PREFIX=/path/to/custom/install/location
cmake --build build
cmake --install build

If you use a custom installation location, you may need to update your PATH:

export PATH=/path/to/custom/install/location/bin:$PATH

Usage

Basic usage:

allele-express <bam_file> -b <bed_file> -r <reference.fa> [options]

Required Arguments

• <bam_file>: Input BAM file (must be indexed)
• -b, --bed-file: Input BED file with target positions
• -r, --reference: Reference genome in FASTA format (must be indexed)

Optional Arguments

• -o, --output: Output file path (stdout if not specified)
• -q, --min-base-quality: Minimum base quality to include in counts (default: 13)
• -m, --min-mapping-quality: Minimum read mapping quality (default: 0)
• -h, --help: Show help message
• -v, --version: Print version information and exit

Output Format

The output is a tab-delimited file with the following columns:

chr  pos  ref  alt  ref_count  alt_count  other_count

Where:

• chr: Chromosome name
• pos: 1-based position
• ref: Reference allele
• alt: Alternative allele
• ref_count: Number of reads supporting the reference allele
• alt_count: Number of reads supporting the alternative allele
• other_count: Number of reads with bases other than ref or alt

License

This project is licensed under the Apache License 2.0. See the LICENSE file for details.

Acknowledgments

• This project uses the argparse library for command-line argument parsing
• HTSlib for BAM file handling
• VS Code Agentic AI with Claude 3.7 for code generation and documentation