Tag Archive | Genesis

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.

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New Compact Chromosome Browser on GEDmatch’s GENESIS

Today GEDmatch launched a version of my segment mapper which is integrated with their database. It can be used as a way to easily visualize multiple matches on GENESIS. This first version shows how everyone compares to the first person on the list, like the current 2D chromosome browser but more compact. Also each color is a person.

My Munson cousins in my new compact segment mapper at Genesis

Above is the screenshot of my Munson cousins which even shows one of the boxes that appears when the cursor is placed on a segment. Click on this image to see a copy of the html version (edited for privacy) where you can put your cursor on any segment to see the details. (N.B. when you put your cursor on a segment and the information pops up via javascript that is called a mouse over in geek speak. )

One way to get a display like this at Genesis is to check the boxes (tier 1 only) next to your best matches in the one-to-many (up to 40 of them) and then click the button “Visualization” at the top of the page. Another way to get there is to use the Tier 1 tool “MultiKit Analysis” and select the kits you want to look at. Remember the first kit listed is the one that all the others will be compared to.

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GENESIS from GEDmatch: the new chip

Technology never stands still. The latest change affecting all of us who love using DNA for genealogy is a new chip from Illumina. The past six or so years of autosomal DNA testing have shown that the current chip is great for testers with European ancestry, but does not have enough SNP coverage to figure out the details of the ethnic make up for people from other parts of the world. Many more and different SNPs are tested in this new GSA chip.

All the 23andMe tests done since this past July use that chip, as does Living DNA (highly recommended if you have British ancestry since it does local regional breakdowns). I imagine eventually the others will follow along. The bad news is that there is not that much overlap between this chip and the previous ones, which affects cousin matching.

Debbie Kennet wrote a blog post describing the new chip at https://cruwys.blogspot.com/2017/08/23andme-launch-new-v5-chip-and-revise.html

Because the SNPs are so different the DNA results from these kits cannot be uploaded to GEDmatch, however our friends there have built another site to handle these new kits called GENESIS. They have come up with a whole new algorithm for relative matching that works with lower SNP counts.

At the recent i4GG.org conference (videos coming in February), I gave a presentation on what’s new at GEDmatch, the second part of it went into much detail about GENESIS, starting with this slide:
http://slides.com/kittycooper/gedmatch-10-13-23#/38

The functions available at GEDmatch are being gradually implemented at GENESIS. Most of the key ones are there now. Plus there is some new functionality. One major addition is the showing of the number of SNPs actually overlapping between kits. Very important to know since the overlaps can be as small as 108,000 SNPs or as large as 580.000.
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