Time to move to GENESIS!

At my recent GEDmatch talk for i4GG, I warned the crowd that soon Genesis would be the only place at GEDmatch where you could upload new DNA kits. Well that day has actually come! Although your kits will migrate from GEDmatch, you may want to upload to Genesis if you cannot wait to see the comparisons. By the way, your GEDmatch login will work just fine at Genesis. Note that Genesis has the GEDmatch logo with an apple core next to it.

So why do you have to move to GENESIS? The problem is that some companies are using newer chips which test for different not completely overlapping markers: LivingDNA and 23andMe since August 2017. Why you may ask? Because the new chips test more SNPs and have more non-European ethnic coverage.

So how do you compare apples to oranges? Well Genesis seems to do a good job of it and the new one-to-many warns you when there are not enough SNPs in common for confidence in the results by highlighting in red. Have a look:

Notice that the last three columns are new. One shows how many SNPs overlap between the kits (in other words, how many SNPs are in common between the two sets of test results so can be compared), the next shows the date compared, and finally the company where the test was done is listed. The latter is needed because kits uploaded directly to GENESIS get assigned kit ids that start with a pair of random letters so the origin is not known from that. Note that migrated kits keep the A,T,M, and H single letters. Also many recently migrated kits will show an overlap of 0 because that has not yet been compared for them.

You may also notice that many columns are missing like haplogroups, gedcoms, and X matching; nor are the columns sortable. Hopefully these features will be added back soon. The display is more compact with the confusing clickable L replaced by clicking on a kit number to see its list of one to many matches. By the way the Tier 1 version of the one-to-many looks exactly the same as the one on GEDmatch.

The new Genesis Home Page

The new home page is more compact and intuitive. I particularly like the new easy editing capability for your kits and that the icons used are explained above them. Just click that little pencil next to a kit to get to a form where you can change the kit from public to research, change your alias, add your haplogroups, etc. It is a good idea if you have uploaded multiple kits for the same person to mark all but one as research, so only the one appears in other people’s one-to-many results. Click here for those slides.

The one-to-one comparison needs to accommodate the different kit sizes and builds so the form looks slightly different. Click here for my slide with a screenshot of the new form. However my favorite new feature there is the ability to see just the fully matching regions (FIRs) which also gives the total cMs. This is only useful when comparing doubly related people like full siblings.

The DNA kit analysis tool shows you how many SNPs will actually be used in the comparisons and how many are slimmed. Missing is the number of no calls.

The rest of the list of DNA Applications includes most of the tools we depend on but is missing the frills like eye color and archaic kits. Gone is the click point for the multi kit analysis (MKA) which is only on the tier 1 menu. However you can always get to the MKA from one to many or the people who match 2 kits. Plus the new MKA selection form is great! There are dropdowns to add in your kits and blanks to add other kits: Click here for my slide on that.

There are many new options in the multi kit analysis, including my pretty and compact chromosome browser which I previously blogged about.

Exciting new features are the ability to triangulate and do matching segment searches on just the kits you have selected in the multi-kit analysis. Sadly though, one of my favorite features, Tag groups, is not yet supported. Also all the GEDcom features are only on the old GEDmatch site at this point.

To see lots of details and screenshots look through my slides from the presentation or wait a month and get the video, purchasable from i4GG.org online.

A possible future tool is a clustering matrix like the ones from Genetic Affairs and now DNAgedcom, stay tuned ..

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27 thoughts on “Time to move to GENESIS!

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  1. i love the new MKA tool. i have been playing around with it. i did a few comparisons with only my first cousins and it is neat to see how we all match each other. i’ve done visual phasing, so i know that the chromosomes that they don’t match me on, they received a segment on that same chromosome from the other grandparent. comparing the visual phasing and the compact tool confirms that. looking forward to the new tools in the future.

  2. I’m confused about the ‘overlap’ column, Kitty. If those in pink/red are lower confidence, why are all of my known cousins and niblings pink? In fact, as I scroll down the page, very few of my matches in that column are not shaded. Tell me, Obi-Wan, my GEDMatch guru. 🙂

    • Kathleen.
      The overlap is how many of the same SNPs are being used for the comparison, nothing to do with how many match each other.
      I will try to make that clearer above

  3. Agree that the reason was a chip change.
    (And WeGene signed up for it too.)
    There was much expectation that more labs would change to that chip, and the old chip would cease production. But that did not happen.
    Nobody is saying why. And it does not really matter.
    We go with what we have.

    Full disclosure would note that LivingDNA have already moved on to a new chip: v2 (easier to remember than Sirius). Is v2 uploadable to Gedmatch?

  4. Do you know the deal with q-matching? It says “revolutionary”, but when I played with it last month I just saw minute adjustments to cM measurements.

    • Guess I figured it out. I am manually phasing with my Dad. With his 1C2R, he shares segments of 5.1 and 5.3 cM with Q values of 26.0 and 24.0. I share a segment of 9.6 cM with a Q value of only 11.0 (higher Q is more confident). My Dad doesn’t share that segment, so it’s a false match, and that is reflected by the much lower Q value. Somehow the algorithm was good at figuring out this segment wasn’t IBD.

      Now I really want to see some histograms of percentages of false-match segments by Q-value. I’m hoping there will be something like Blaine Bettinger’s self-reported matching data, but for Q-values and whether a match is known to be false or true. I would trust such tables more because at least the data would all be coming from the same site and algorithm, even if it is still self-reported.

  5. Thanks, Kitty. You solved a problem for me. I had a kit in GENESIS that was listed on my homepage summary with an “N” next to it, just like your kit for Lawrence Munson has an “R” next to it in your illustration above. But there’s no explanation in the legend as to what the “N” means. From this blog, I learned that I can click on the pencil icon and look at the corresponding profile. Doing that, I found that the kit was not for public access. I changed it and all is well; the “N” went away. I don’t know how it got to be non-public in the migration; it was public on the old GEDmatch. Thanks for this blog. You also have a better explanation of what “overlap” means than I have seen anywhere else.

  6. “Move to” is not an unambiguous term.

    The old GEDmatch still appears to work in all its glory.

    On the other hand, their are certain types of data that won’t work there so we have to use Genesis if we want to include them. A few weeks ago, the GEDmatch team asked me to upload a number of my old kits to Genesis and I did what I could under the circumstances. So now when I use Genesis, I will see these kits twice. (They asked me to do that as part of an attempt to automate analysis of endogamy, which I feel to be an impossible task, involving circular logic.)

    The waters are becoming muddy indeed.

  7. I’m first time user of GEDMatch, attempting to upload raw DNA results to Genesis. I filled-in all the blanks, including checking the circle saying I’m authorized to upload. I chose the correct file, then clicked on the Upload button. A warning message block then appeared near the top of the screen “genesis.gedmatch.com says This DNA must be yours or you are authorized to upload this DNA”. I clicked “OK”, but nothing happens. I clicked upload, same warning message reappeared. I then experimented, instead checking the circle “the DNA is yours.” I received the very same warning message and clicking “OK” still did nothing. What am I doing wrong?

    • Found my mistake. I overlooked another nearly identical question that also needed a circle check. I clicked them both and it worked. Sorry to trouble you.

  8. Hi Kitty! I find this blog fascinating, as I have just begun my bio family hunt. I’m a little confused as my top people are still pink and red in color but have cM above 70. Since I am likely looking at half-relatives, could this explain some of that? On 23andMe, I have 1.26% and for some of these, which can mean 2nd or 3rd cousin in a situation where there are half-relatives. Correct? Any help would be appreciated.

    • Rachel
      the pink and red just mean that the testing companies do not have enough common SNPs (the overlap) to be confident in the results of the comparison. Nothing to do with whether they are half relatives.

  9. Great blog! It appears the Genesis “one-to-many” report shows many more matches than the original GEDmatch report which listed your top 2000 matches. Is this the case?

  10. They’ve taken away DNA paint for new downloads? The one feature that changed how I might answer the ethnicity question? A bunch of numbers on a spread sheet and a hazy explanation about how the population relates to those figures just causes more confusion. DNA paint was/is ahead of its time. What a shame.

    • Brad,
      Gedmatch and genesis run on the web so no need for a Mac version. You may however need to use the chrome browser. Another issue Mac users sometimes have is the automatic unpacking of zipped files. You may want to change that setting since You need to upload DNA results files zipped

  11. I find the x one to one on genesis really difficult to interpret. It has breaks in the x where there should be any, and for two woman, who are full siblings it is hard to see the fully identical segments. The regular one to one provides a lot of good information, including percentage of fully identical. The x one to one does not.

    • Cathy –
      Due to chip differences and the new template even full sisters show a break in the middle of the X from about 52M to 65M plus sometimes at the ends. As long as the total is 189cM or more that is ok.

  12. Hi, since uploading to Genesis, I noticed that my one-to-many results stop at 3000 matches, which means all of my 7 cm matches dropped off my list. I can still see the match when I compare these kits as one-to-one. Is there a way to remove (from display) the kits that were migrated? Or does Genesis plan to combine the duplicate uploads?

  13. Will we be able to manipulate the data to see past the 7.5 generation in Gedmatch Genesis as we can in Gedmatch.com?

  14. It appears that the matching segment routine default settings produces only the top 1000 matches, about half of the old tier one routine output. Is this actually the case?

    • Jenny
      Yes – buy a month pf tier 1 if you want to see more matches. At $10 that is a bargain and it osis far from free for them to run the site

  15. I’m a little confused, as I have not been notified by GEDMatch on what to do with my account and my uploaded DNA. Question 1a) Will GEDMatch automatically transfer my raw DNA to Genesis ? Question 1b) Do they transfer a copy of my raw DNA to Genesis and leave my original at GEDMatch? Question 2) Will I need to eventually delate my raw DNA from GEDMatch as the site will become obsolete? Question 3a) If I have to upload my raw DNA file to Genesis, do I need to create a new separate account with Genesis? Question 3b) What new advantage will I gain if I upload my raw DNA instead of letting it be transferred? Thank you!

    • Tyia –
      1a) All kits have now been transferred
      1b) The classic gedmatch will be around for a while and has your original kit data still
      2) no need to delete, eventually the old gedmatch will be gone
      3a) your same username and password from gedmatch will work at genesis
      3b) The matching may be a tiny bit better if you upload your data again to genesis since the comparison template is different and the old gedmatch did not keep your raw dna results but rather converted from the template of how they stored it there

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