# WGS Extract (WGSE.bio)

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.

WGS Extract User Manual : v4 User Manual (Google Doc)

Latest Releases you can install on the supported platforms are:

Track | Version | Date | md5 hash signature
--- | --- | --- | ---
BETA v4 | 44.5 | 13 Jun 2024 | fbe59361caaf8cdb6f23df16a249c552
ALPHA v4 | 44.6 | 20 Jun 2024 | c3c6a283dec9fa0dce66a6210adfb04d
Dev(eloper) v4+ | 44.9 | 30 Sep 2024 | f69b432ef8ebe2364b7c66283bc314bb

These are just the installer scripts. Installation Section in the user manual for 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. hashes to verify the Installer you download .

> - With MacOS Sonoma 14.5 and later, Apple MacOS regressed and turned off allowing unsigned apps to be downloaded and run from outside their store. `sudo spctl --master-disable` . For older releases, the first time you run the app, follow the Ctrl-Click process from before as described in the manual.
> - With MacOS Sequoia 15.0 they have permanently removed the “anywhere” option completely. “Install_macos.command” was blocked to protect your Mac. with a button next to it that says “Open Anyway”.
> - Ubuntu 24, MacOS 14 and MacOS 15 require release 44.6 or later.

This tool is geared toward the needs of genetic genealogy and Ancient DNA (aDNA) studies but can be helpful for those looking into health-releated 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 . Many health analysis sites accept the microarray and VCF files generated by this tool.

> Still waiting for your WGS test results? 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.

This tool is designed to be a simple, push-button manipulation of WGS files from any source. UseGalaxy ).

Dante Labs , Nebula Genomics , Sequencing , and YSEQ are test results most commonly used with this tool. Full Genomes Corp , GeneDX , Sano Genetics and Veritas (historical) are other test providers whose output is processed here. These are all results from Illumina and MGI next generation sequencers ( NGS ). Results from Oxford Nanopore and PacBio HiFi CCS third generation, long-read sequencers can also be used; as can FamilyTreeDNA ’s BigY output. (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 encourage the use of the Facebook group Personal WGS for discussions on how to make use of your personal, sub-$500, DTC 30x WGS test results. 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. Developer’s should visit the main GitHub WGS Extract Developers Code Repository as well. Development issues, Alpha code bugs and limitations should be raised in the development issues section so they are tracked till resolved in a release. Program folder for the Python source files.

There is a separate Reference Genome Library manager that can be run to check and update the library. The WGSE program will check and determine when it needs a genome and prompt you to install any missing file then.

v4 entered Alpha on 1 April 2022 and was formally Beta released on 6th November 2022. v5 entered pre-Developer mode release on 10 March 2023 and had a first real release in July then Nov 2023. Old releases are documented in the historical release section . (v5’s release in Dev has been delayed.)

The tool home page is WGSE.bio . With the developers and delivery platform using WGSE.io (note the slight difference; they will cross reference each other). Currently, both point to this page located at https://WGSExtract.github.io/ .

# Supported Platforms

64 bit OS and processor platforms tested as part of the release process are:

- Microsoft Windows 10 and 11 on Intel and AMD 64 bit processors using Cygwin64 and soon Msys2 packages for the bioinformatic tools. WSLG in Win11 with a Linux Desktop (not server) can be used to install the Ubuntu or Linux release of this tool.
- Apple MacOS 11 (Big Sur), 12 (Monterrey), 13 (Ventura), 14 (Sonoma) and 15 (Sequoia) on Intel and Apple M1/M2 processors. (note: We rely on Macports which has dropped support for Catalina and earlier already)
- Ubuntu Linux LTS 20.04, 22.04 and 24.04. We recommend 24.04 to get the latest Samtools release.
- Any Linux by using Conda (actually micromamba and bioconda). This will soon deprecate the Ubuntu only installer and is the preferred Linux install method.

The tool has the potential to be a simple install in a BioConda environment as it is mostly just a Python package .

# Thanks

- To the JetBrains / PyCharm community for the support of a Pro developers license for this and other open-source projects
- To the Github community for their free support to open source projects like this one

# Windows Release Users

Some have downloaded the WGS Extract tool solely to gain access to the MS Windows native executables of the Bioinformatic Tools we include. You can use these Bioinformatic tools independent of the WGS Extract program. 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. WGSE .

Windows 11 WSLG with Ubuntu Linux Desktop (not server) can be used to install and run WGS Extract . You have to tune WSLG parameters to get effective use of your disk space, CPU cores and memory under WSLG.