WGS Extract WWW home
is a desktop tool for verifying, analyzing and manipulating your Personal 30x WGS test result. It can also be used with any human genome based BAM or CRAM file including WES and Y-only test results. It is often used to extract a microarray test file from 30x WGS results for analysis by other tools.
Latest Releases you can install on the supported platforms (pre-v6 or v6) are:
| Major | Minor | Date | md5 hash signature | User Manual (google doc) |
|---|---|---|---|---|
| v4 | 44.15 | 20 Oct 2026 | 8e54cf339d0a3407d5dd82d081747fbe | v4 |
| v5 | 48 | 30 Apr 2024 | (not yet available) | v5 |
| v6 | 0.6.6 | 6 Nov 2026 | (signed, self-checking installers) | N.A. |
The new v6 is a heavy-AI rewrite of the original with a big expansion of capability. All bioinformatic tools are natively re-compiled as stand-alone, optimized, and vetted. New application documentation is not yet available. The CLI can be discovered by command-line querying. The old user manual can be helpful for GUI users trying to understand previous, common functions still available.
For v4 and v5: Version and Date above is for the Program package. The installer version and date is different.
See the Installation Notes below for platform support of different versions.
Facebook groups Personal WGS and WGS Developers for discussions on the tool.
This tool is geared toward the needs of genetic genealogy and Ancient DNA (aDNA) studies but can be helpful for those looking into health-related uses of WGS tests. The personal, sub-$500, Direct-to-Consumer (DTC), 30x Whole Genome Sequence (WGS) tests are delivered with basic data files and reports. This tool serves to bridge the gap between the WGS data files delivered and the present day genetic genealogy community tools.
We specifically do not do post-VCF analysis for health. But there are other sites that do (google doc). Most health analysis sites accept the microarray and VCF files generated by this tool.
Ancient DNA or recent samples from research studies (e.g. 1K Genome) are often processed with this tool.
Still waiting for your WGS test results? Want to get started today? See the International Genome Sample Resource (1K Genome archive) for BAM or CRAM files that you can download and play with to learn the tool while waiting for your results.
Note: while the tool processes low-coverage sequencing files available from some genetic genealogy vendors, it does not yet have the mathematical modeling (e.g. imputation and bias correction) to truly make them useful.
This tool is designed to be a simple, push-button manipulation of WGS files from any source. It hides the installation and scripting of complex bioinformatic tools and automatically adapts based on the data within your files. For more control over your pipeline, either learn to use the underlying tools or seek out a Galaxy server (such as UseGalaxy). As of 2026, the Forensic Genetic Genealogy market has developed their own, similar tool for use in law enforcement settings. But it uses imputation and starts from FASTQ/BCL files only.
Dante Labs, Nebula Genomics, Nucleus Genomics, Sequencing, tellmeGen, and YSEQ are test results most commonly used with this tool. Full Genomes Corp, GeneDX, Sano Genetics, Invitae and Veritas (historical) are other test providers whose output is processed here. These are all results from Illumina and MGI / Complete Genomics next generation sequencers (NGS). Results from Oxford Nanopore and PacBio HiFi CCS third generation, long-read sequencers can often also be used; as can FamilyTreeDNA’s BigY output. MyHeritage new low-coverage WGS CRAM replacing their microarray test and their future DNA360 30x WGS files work here. MyHeritage are processed on an Ultima Genomics sequencer which requires a modified pipeline which we have now included. The FamilyTreeDNA new Family Finder Twist Biosciences enrichment NGS result CRAM (if and when they provide it) should be processable here also. (This is not an endorsement of any company or service; simply reporting what is commonly used with the tool.)
The tool acronym is WGSE and pronounced as “wig-see”. We encourage that use in conversation.
We use of the Facebook group Personal WGS for discussions on how to make use of your personal, sub-$500, DTC 30x WGS test results. Bugs, use cases and announcements about the main tool happen there. As part of that groups’ Files section, you will find a number of useful companion documents and tool references. In particular, see Bioinformatics for Newbies. We also maintain a number of corrollary documents.
User issues, if not brought up in the Personal WGS Facebook group, should be raised in the local user issues section of this GitHub site. The issues section is preferred so code bugs, use limitations and suggested improvements can be tracked within the development project.
There is a separate Facebook group for WGSE Developers and Alpha testers where bleeding edge issues are discussed and tested before wider availability. For v6, everything is handled in the WGS Extract CLI repository. Development issues, bugs and suggestions for improvement should be raised in the v6 issues section. For v4-5, developer’s should visit the main GitHub WGS Extract Developers Code Repository. Development issues, Alpha code bugs and limitations of v4-5 can be raised in the development issues section so they are tracked until resolved in a release. If you want to take a stab at modifying and improving the code, then the manual contains many suggested improvements. If the latest release is not checked in to GitHub, simply download the latest release files and start from there. Look in the Program folder for the Python source files.
v6 was very preliminarily released in Feb 2026 and encourage for general use starting in Nov 2026. v5 entered pre-Developer mode release on 10 March 2023 and had a first real release in July then Nov 2023. v4 entered Alpha on 1 April 2022 and was formally Beta released on 6th November 2022. v1-2 older releases are documented in the historical release section and date back to mid-2019.
The tool home page is WGSE.bio. With the v4-5 delivery platform using WGSE.io (note the slight difference; they will cross reference each other). v6 is delivered directly from githubhttps://github.com]. Currently, both point to this page located at https://WGSExtract.github.io/.
The ZIP archives linked above are just the installer scripts. You need to download, unpack and run the installer script for your OS. See the Installation Section in the v4 user manual for specific details about installing on your platform. See the v4 Release Notes in the installation directory for more information about the updates in the current release. You should periodically re-run the installer to update to the latest release in the track you select. There is information available on how to use hashes to verify the Installer you download.
- Starting with MacOS Sequoia 15.0, Apple has permanently removed the option to allow for non-signed installs. The only way to run non-app-store and non-apple “notarized” apps is, within 30 minutes of downloading and trying to open the first time (and clicking Done in the pop-up that comes when you try to run it), you must navigate to systems settings / privacy & security and scroll all the way down to the Security section. You should see “Install_macos.command” was blocked to protect your Mac. with a button next to it that says “Open Anyway”. Once clicked there, you will then get the old “open anyway” pop-up to finally approve the program. You will also be required to enter your password in a follow-on pop-up to approve the action. You must do this each time you download and install an update as well.
Some have downloaded the WGS Extract tool solely to gain access to the MS Windows native executables of the Bioinformatic Tools. You can use these Bioinformatic tools independent of the WGS Extract program. Look in the cygwin64/usr/local folder for the bioinformatic tools. Just add cygwin64/bin and cygwin64/usr/local/bin to your PATH to make the programs available from the Terminal command line of CMD, Powershell or BASH. If you do not wish to use the rest of the WGSE release, just delete everything except the cygwin64 folder and adjust your path for wherever you move the folder. For those using the new Msys2 release, it is the msys2/usr/bin and msys2/ucrt64/bin folders; respectively.
Since v4, this is a full, BASE environment of Cygwin64 that is captured as of the stated release date. The bioinformatic tools are compiled to this same version on that release date. So do not update the cygwin64 libraries else the bioinformatic tools will break. Msys2 is just a minimal set of tools to operate WGSE.