Playing with Genoplot

I discovered a fun new DNA data visualization tool that is not only an awesome alternative to the completely outdated GEDmatch reports and visualizations, but packs some cool extra features that are not obvious at first glance, including running your own admixture calculations or user-contributed models on various samples, and plotting custom PCAs.

Genoplot is visually pleasing, but is not very intuitive… Also, there’s a trick you need to know to actually load your own samples into the additional tools beyond the standard admixture. So here’s a step-by-step guide to get you started.

In the top right corner we have a menu (in addition to info on the company and their privacy policy, of course)

You want to start with the ADMIX CALCULATORS option

Now, you can ADD a DNA file from you hard drive. They will take a number of different formats, including 23andMe, MyHeritage, FTDNA, and Ancestry. You can also generate a personal security token to encrypt your file.

Once you add the files you want, you’ll chose HarappaWorld K16 calculator first and run it for all your personal samples

You’ll get a cool radial chart like this, and you can click the center for Oracles

You can then run whatever else you want on this page, as long as you have the compute credits to do so :) I think you start with 100 and can get 1000 for $2.

Then we’ll switch to the NMONTE RUNNER page

First, switch from Global 25 to HarappaWorld

Then click on the EDIT icon in the top right corner there

You then “edit sample” for each of your files uploaded

Here’s where we can simulate the data needed for the other tool by enabling the “Create G25 Simulation” toggle button

Press “Modify” and then “Save”

Once this is done, your samples should appear in the dropdown!

And you can run your own or pick one of the existing calculators that you can’t find anywhere else

You can switch the MODE under the SAMPLES box for different options. I found some cool ones based on linguistics and such

Finally, go to PCA PLOTS in the main menu

You can select all your samples to appear in the plot

And any groups or individual historical DNA samples you want to compare. Availability will depend on the MODE selection here as well.

And then you PLOT!

You can use all the samples to keep it real or just plot the averages for a cleaner view :)

ENJOY!

P.S.

I’ve discovered that once you get your simulated G25 coordinates, there’s a whole other set of calculators and PCA plots you can run over at http://vahaduo.genetics.ovh / https://vahaduo.github.io/g25views/ !!!

I’m a Caltech particle physics PhD turned Data Scientist, currently working as an independent consultant.