A tool for processing whole genome sequencing (WGS) data files. Supports BAM/CRAM analysis, microarray file generation, and Y/MT haplogroup determination.

• BAM/CRAM file analysis with coverage statistics and reference genome detection
• Microarray RAW file generation (23andMe, AncestryDNA, FTDNA, MyHeritage, etc.)
• Y chromosome haplogroup determination using Yleaf
• Mitochondrial haplogroup determination using Haplogrep
• Reference genome library management with automatic downloading
• MT/Y chromosome extraction to FASTA, BAM, or VCF

• Linux, macOS, or Windows
• 8 GB RAM minimum (16+ GB recommended)
• 50 GB free disk space (200+ GB recommended for reference genomes)

• Python 3.11 or later
• samtools 1.10+
• bcftools 1.10+
• tabix 1.10+
• Java 8+ (for Haplogrep)

Ubuntu/Debian:

sudo apt install samtools bcftools tabix default-jre python3.11 python3.11-venv

Fedora/RHEL:

sudo dnf install samtools bcftools htslib java-latest-openjdk python3.11

macOS (Homebrew):

brew install samtools bcftools htslib openjdk [email protected]

Windows:

• Python: https://www.python.org/downloads/
• samtools/bcftools: https://github.com/samtools/samtools/releases
• Java: https://adoptium.net/

./setup.sh

setup.bat

The setup script creates a Python virtual environment, installs dependencies, and configures the bundled Yleaf tool.

./wgsextract.sh

wgsextract.bat

1. Load a BAM/CRAM file from the Settings tab
2. Download a reference genome matching your file (Settings → Reference Library)
3. Use Extract Data tab for microarray generation or chromosome extraction
4. Use Analyze tab for haplogroup determination

wgsextract/
├── core/           # Configuration and logging
├── services/       # BAM analysis, microarray generation, haplogroups
├── gui/            # PyQt6 user interface
├── models/         # Data structures
└── utils/          # Utility functions

reference/          # Reference genome catalog
yleaf/              # Bundled Yleaf 3.2.1 (Y haplogroup tool)
tools/              # Haplogrep JAR file

• 23andMe (V3, V4, V5)
• AncestryDNA (V1, V2)
• FTDNA (V1, V2, V3)
• MyHeritage
• Living DNA
• National Geographic (Geno 2.0)
• CombinedKit (all available SNPs)

GNU General Public License v3 or later

• Yleaf: Y-chromosomal haplogroup assignment tool (Ralf et al.)
• Haplogrep: mtDNA haplogroup classification
• htslib/samtools/bcftools: BAM/VCF processing libraries