Install
Install the standalone app or use Pixi directly
Use the standalone macOS/Linux installer, the native Windows installer, or the developer Pixi workflow when you want a normal source checkout.
Read the install guideLocal-first genomics toolkit
Turn whole genome data into useful files, reports, and extracts.
WGS Extract CLI is a modern, scriptable command-line recreation of WGS Extract. It wraps common bioinformatics tools so you can inspect BAM/CRAM files, build consumer microarray files, call variants, extract Y/MT reads, manage references, and automate repeatable genome work.
A practical reference site, not just a splash page.
Use the pages below as a map for installing the tool, understanding WGS file types, and running common genome workflows safely.
CLI reference
Command groups and recipes
Learn the major command families for info, BAM/CRAM, extraction, VCF calling, annotation, lineage, FASTQ QC, references, and fake data.
Open the CLI guideGraphical interface
Want a GUI?
This package is CLI-only. Use gui-for-cli when you want a graphical interface for these workflows.
Workflows
Go from a goal to commands
Follow recipes for microarray simulation, Y-DNA and mtDNA extraction, variant calling, FASTQ to BAM, storage conversion, and testing.
Pick a workflowWGS guide
Learn whole genome concepts
Get a friendly explanation of whole genome sequencing, coverage, references, variants, file types, read technologies, and interpretation limits.
Read the WGS guideReference
Glossary and safety notes
Look up common terms, file extensions, external tools, privacy considerations, and troubleshooting tips for long-running genome jobs.
Open the reference