To use your whole genome file on Genetic Lifehacks, you will need to convert the data into a format that looks like 23 and Me or AncestryDNA raw data. The converted whole genome file that contains all the SNPs from 23andMe and AncestryDNA will fill in all the blanks on Genetic Lifehacks.
This article covers how to convert the full genome BAM to a .txt file in the 23andMe format using a free software tool called WGSExtract. I recommend doing this on a desktop or a fast laptop computer due to the file size and storage needed.
If you can’t use the WGSExtract software and do the conversion yourself:
Genetic Lifehacks file conversion service
This is an option offered to members at a nominal fee.
Perfect for those who can’t do the file conversion themselves.
Converting the BAM file using WGS Extract:
To convert the whole genome BAM file, I used WGS Extract, which is a free, open-source software:
https://github.com/WGSExtract/WGSExtract.github.io
A detailed instruction manual is available on the GitHub page (100+ pages).
Yep, this is one of those times that you will need to read the manual. The software is a bit rough around the edges regarding the user interface and installation. The plus side is that the application is free, works well (I’m on a Mac), and does exactly what is needed.
Follow the installation instructions for your operating system.
Note: For the reference library for a Dante Labs whole genome, use hs37d5. It was option 13 in WGSE v3.
After installation and before converting a file, you’ll need to be sure to set the Output Directory first. Choose a folder that is different than the one that contains your .BAM or .CRAM file.
Once WGSE is installed and running:
1.) Select your BAM file on your hard drive. (If you’re using Nebula data, use the CRAM file)
2.) When you load in your Dante Labs BAM file, it will pop up an alert that it needs to be indexed. (The Sequencing.com or other .BAM files may already be indexed, so you could skip ahead to step 4.)
Click on the Index button next to where it says Statistics and Attributes:
3.) Now, wait 30 minutes or so to generate the BAM index file. It didn’t take quite that long on my computer. You can do other things on your computer while waiting, but don’t close the application or the terminal window.
For example, you can read through the manual again while you wait… :-)
4.) Key: Once you’ve indexed the BAM file, you will need to click on the Stats button before you can do anything else. Yes, it clearly says this in the manual, but I missed it and was confused for a bit.
5.) Next, click on “Extract Data” and then on the “Microarray RAW” button.
To use the Genetic Lifehacks membership features, either choose 23 and Me v4, v5, and Ancestry v2 — or — select Combined file. There are many other options to come back later and play with here.
6. Click the Generate button.
It will give you an expected wait time for the processing. Mine said 50 minutes, but it took about half that.
Your data files should now be in the folder that you set up for WGSE to use.
7. That’s it! You should be able to connect on the Member’s Start page to the new raw data file. If you are already using a different raw data file, you must first hit the “Clear Data” button before connecting to the new data file.