WGSExtract.github.io

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WGS Extract

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 test results; albeit with a more limited benefit.

WGS Extract User Manual: v3 Beta, v4 Alpha (Google Doc)

Latest Releases you can install on the supported platforms are:

See the v3 Release Notes and the Installation Section in the v3 Manual for more details on changes or installation particulars for your platform. v4 release notes are inside the release directory.

A flaw was introduced in the v4 Alpha code on 22 June 2022 and only discovered on 8 Aug 2022. All v4 release files have been patched to fix the issue within the microarray generator. If you have trouble converting the CombinedKit into 23andMe v3, etc using aconv.py, then simply delete your program/ folder and rerun the installer. This will update your v4 system with the patch.

This tool is geared toward the needs of genetic genealogy but may be helpful for those looking into health-releated uses of WGS tests. The 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 from your WGS test by 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.

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 determines the needed parameters based on the data within your files. For more control over your pipeline, either learn to use the underlying tools directly or seek out a Galaxy server (such as 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 or MGI next generation sequencers. Results from Oxford Nanopore and PacBio HiFi third generation 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 use the Facebook group Consumer WGS Testing for discussions on how to make use of your sub-$500, DTC 30x WGS test results. Bugs, use cases and announcements about the Beta release tool happen there. As part of that Facebook groups’ Files section, you will find a number of useful companion documents and tool references. In particular, start with Bioinformatics for Newbies.

User issues, if not brought up in the 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 Developers and Alpha testers where bleeding edge issues are discussed. Developer’s should visit the main GitHub WGS Extract Developers Code Repository as well. Development issues, code bugs and limitations should be raised in the development issues section so they are tracked till resolved in a release. The manual contains many suggested improvements if you want to take a stab at modifying and improving the code. If the latest release is not checked in to GitHub, simply download the latest release and start from there. Look in the Program folder for the Python source files.

With v4, we have opened the following three release tracks to all: Beta, Alpha and Dev(eloper). Chose the installer for the track you wish to be on. Then simply rerun the installer when you are ready for an update to get the latest available release for that track. Developer releases are every few days to weeks and minimally tested. Alpha releases every few weeks to months and tested on each release platform with some key, new features not yet complete. Beta releases are every quarter to year and extensively regression tested and self consistent in their feature set.

If you want to change release tracks at anytime, simply edit the release.json file in the installation directory to change to the desired release track and then rerun the installer. Or overlay the new installer downloaded from above onto your existing installation. The only difference in each installer is the release.json file and its track setting inside. Your current, installed version is displayed at the top of the program when run.

We bring you v4 some 13 months after v3. The original, first 2 years v1 and v2 historical release from Marko is documented there. v3 went into Alpha on the 18th June 2020 and was finally released as Beta on the 15th June 2021. v4 entered Alpha on 1 April 2022 and has yet to be Beta released.

This page is located at https://WGSExtract.github.io/ and serves as the WWW home for the tool. As the need develops, we will create our own Facebook Group for users to raise issues outside of the local User Issues Section already mentioned.

Supported Platforms

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

The tool has the potential to be a simple install in a BioConda environment as it is mostly just a Python package. But a majority of our users are on Microsoft Windows 10/11 systems. Bioconda nor the bioinformatic tools are supported there. So we currently deliver the tool with our own installer and Windows executables as needed. This may change going forward after we find a Windows package manager to supply the bioinformatic tool ports we currently create. This is the only source of the current bioinformatic tools on a Windows system (that we are aware of). Docker packages are either not usable across all the platforms or too ineffecient at the current time for these large file and program needs. But could play a role in the future.

Thanks

Windows Release Users

Some have downloaded the WGSE tool solely to gain access to the Win10 native executables of the Bioinformatic Tools that we make available. These are installed on Windows systems. You can use these Bioinformatic tools after installing the WGS Extract program on Windows. Look in the cygwin64/usr/local folder are all the bioinformatic tools. Just add cygwin/bin and cygwin/usr/local/bin to your PATH to make the programs available in the command line.

In v4, this is a full, BASE environment of Cygwin64 captured as of the stated release date. The bioinformatic tools are compiled to this same versions on that release date. So do not update the cygwin64 libraries else the bioinformatic tools may break.

The CygWin64 tools natively compiled to a Windows platform can be slower than native Linux binaries on the same platform. The Windows WSLG environment with Ubuntu Linux using the Linux versions of the bioinformatic tools can be installed and used also. Once WSLG becomes more complete and supported in Windows 11, we will likely avoid delivering Windows executables all together and simply ask Windows users to install and use WSLG for running WGS Extract. At which time we can consider becoming a Bioconda package as well. We do not provide support for the use of WSGE on WSLG at this time. Recent changes in the WSL2 file system in the last year finally made WGSE on it possible and generally faster than the Cygwin64 native binaries. This occurs because Windows kernel cannot support some fundamental features the bioinformatic tools rely on (e.g. memory mapped files).

SHA256:   TBD
 *WGSExtract-Betav3_10Jul2021_installer.zip (patched)
 *WGSExtract-Alphav35_31Jul2022_installer.zip (may not be same version available above)
MD5:      TBD
 *WGSExtract-Betav3_10Jul2021_installer.zip (patched)
 *WGSExtract-Alphav35_31Jul2022_installer.zip  (may not be same version available above)

More information is available on using hashes to verify the download