GEDmatch tools 2016

Recently I gave an updated talk about GEDmatch.com for my local DNA special interest group, DIG, here in San Diego. GEDmatch.com is a DNA geek’s playground, but many less computer inclined folk find it difficult at first.

My Favorite GEDmatch Tools

It is the only place for those who have tested at Ancestry DNA to compare their results to a possible relative, chromosome by chromosome. It also has many tools that are unique such as ancestry composition calculators with more recent breakdowns and more categories than the main companies. I covered those in detail in my original talk about GEDmatch tools. Those slides are at http://slides.com/kittycooper/gedmatch#/5

The new talk – http://slides.com/kittycooper/gedmatch-10#/ – covered uploading your data, how to manage your kits and mark a kit for research, and much detail on the one-to-many function as well as all my other favorite tools (starred in the image to the left).

There is a new 23andme upload which is nice and fast as it uses the API so you actually log into your account there rather than uploading a file.

It makes sense to upload all your kits when you have tested at more than one company but please mark all but one kit as research only, so DNA relatives are not confused by seeing so many versions of the same person.

 

To mark your kit as research only you click the link EDIT or DELETE your DNA resource profiles at the bottom of your list of kits. Then select a kit to edit. On the next screen you check a box to mark it for research only. Keep the kit with the most SNPs as the public one. You can use the DNA File Diagnostic Utility to check which that is. Probably that is your Ancestry kit unless you tested at 23andme before December 2013

Why have more than one kit? Well they each test slightly different SNPs so it makes sense to compare apples to apples not oranges. In other words, if you have a new DNA match that has tested at a specific company you want to compare them in the one-to-one with your kit from that same company for slightly more accurate results.

The one-to-many uses lower thresholds than the defaults for the one-to-one comparison, so I usually lower the SNPs to 500 and the cMs to 6 when I do a one-to-one, but take the smaller matches that show up with a grain of salt …

The one-to-many is the most important tool of all. Use it to regularly check for new close matches. I went over what each column is and discussed the generations listing. Note that you can sort any column by clicking the blue arrow at the top of that column. Normally it is sorted by total cMs. Here are the columns explained.

Heading Explanation
Kit Nbr The kit number: Ancestry kits start with A, 23andMe with M, Family Tree DNA with T, MyHeritage with H, and others with a Z
Type The companies change chips occasionally so this tells you which version, V4 is the current version for 23andme
List Not what I expected, clicking this gives you the one to many for that kit
Select You can select a group of kits with this box, then click submit at the top and have many comparison options
Sex If the user did not put it in you see a U, else F or M
Haplogroup there is a column for the mtDNA haplogroup and the Y haplogroup, self reported.
       AUTOSOMAL
Details Click the A to get the one-to-one autosomal report
Total cM For close family, total cM will follow Blaine’s charts at ISOGG well,  up to 3rd cousins
largest cM For endogamous groups I recommend sorting by this column (the blue arrow at top)
Gen Subtract one to get the cousin level. So 4 means a 3rd cousin. A nephew or uncle will be 1.5
       X_DNA
Details Click the X to get the one-to-one X report.
Total cM Total matching cMs on the X.
largest cM Largest segment on the X, as X can reach very far back in time so only look at the large matches initially
Name the name or pseudonym of the person
Email email address to use for contact

In the generation listing your parent or child is 1, an aunt or niece is about 1.5, a grandparent is 2, for cousins subtract one from the number so if it shows generations of 4, the suggestion is 3rd cousin. My recommendation is to follow up with anyone who is 4.5 or less. Start with the closer ones. Accuracy in autosomal matching declines after 3rd cousins. I showed Blaine Bettinger’s chart for estimating a relationship from total shared cM (this has been updated recently see http://thegeneticgenealogist.com/2016/06/26/update-to-the-shared-cm-project ).

You can do a one-to-one from the one-to-many by clicking the A. I included a number of examples including my Dad at two different companies (note the small breaks!). Also two full siblings will have many green bars, places where they are fully identical because they inherited the same DNA as each other on both paired chromosomes from each parent.

A very useful feature is to select a group of people from the one-to-many and then look at all of them together in various chromosome browsers. Also you can get a CSV of their matching segments that compares everyone in the group to everyone else. Since it is sorted by person this is a quick way to add match information to your master spreadsheet or to start a spreadsheet if you tested at ancestry.

#D chromosome browser image

The 3D chromosome browser

I went over the 2D chromosome browser, also covered in my blog post here which compares everyone to just the first person in the list (you?). Next we looked at the 3D browser which compares everyone in the list to each other. You have to select each chromosome one by one.

After the one-to-many and the one-to-one, I find the ”People who match one or both of 2 kits” most useful. It is a quick way to see which family line a new relative is part of by who else they match.

Finally at slide 36 I got to the paid, tier 1, utilities.

I use the matching segment search when I am interested in a specific segment. You used to be able to specify the segment but so few people used it that way that they turned into a listing of all your overlapping segments.

The relationship tree only works if you have X and it was an experiment.

Of course, my favorite in tier 1 is the triangulation tool(see my post on that). I suggest selecting both options the first time you use it. Then run it again with just the sort by kit number because you can cut and paste that to a spreadsheet and then sort by chromosome and start point to see the triangulation segments

I mentioned the lazarus tool where you can construct a kit or partial kit for a dead ancestor if you have enough descendants and relatives tested but did not have time to go into its details.

21 thoughts on “GEDmatch tools 2016

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  1. Pingback: Favorite Reads of the Week: 2 July 2016 – Native American DNA, Township Records, Bibliography of County Histories – Family Locket

  2. I AM LOOKINGVFORWARD TO MEETINGBAND BRING MATCHED TO MY RELATIVES. Kitty I HEARD YOUR BLOG IS THE BEST. SHOW ME.

  3. Thank you for your blog. It is so incredibly helpful.

    Most GEDmatch tools are free. Seems too good to be true so I’ve been asking myself “what’s the catch?”. The “Future” section of their site policy intrigues me:
    “We cannot predict what the future holds for DNA or genealogy research. We cannot predict what the future will be for GEDmatch. It is possible that, in the future, GEDmatch will merge with, or operations will be transferred to other individuals or entities. If that happens, the operating personnel at GEDmatch will change. That event would provide access to your data by people not currently involved in GEDmatch operations. If this possibility is not acceptable to you, please do not upload your data to GEDmatch. If you have already uploaded your data, please remove it from GEDmatch.”

    I think it may inform us about why the site is free and I’m wondering about your take. Is GEDmatch collecting data and fine tuning its tools in order to sell the database and the tools to another entity or to eventually transition from a volunteer platform to a paid commercial platform? In other words, are users participating in GEDmatch’s research and development for future profit, rather than paying them in money?

    • I agree. They have to state that for legal purposes, and to protect themselves from lawsuits. There is no “certainty” in this world–that is why insurance is one of the largest industries. Tomorrow is not only unpromised…it’s unknown.

  4. I have just discovered your blog and I love it!!! Thank you.
    I am somewhat new to all of this and I hope this is not a ridiculous question to ask. Once you have uploaded your raw DNA to GEDmatch I do not understand how to get your GEDmatch file so that you can put it on places such as Familysearch and other places. Would you be kind enough to explain this or point me in the right direction? Blessings to you.

  5. Is it possible that two 1/2 sisters will share their x-match as two separate? 151.8 + 44.3 =196? or should it be one entire unbroken x?
    2032 cm across 60? Thanks!~

    • Two half sisters who share a Dad should have an unbroken X match BUT if there is a tiny error or series of no calls there could be a false break shown making it two segments. What company shows the break? GEDmatch usually ignores the no calls so it would be unbroken there.

  6. If I run the Gedmatch kits at differing times, will the results, in the reports change? Is new dna/genomes being updated in all of the GEDmatch reports? I noticed many reports were deleted in the MDLP.

    • More kits are added to the GEDmatch database every day but the time of day should not affect your results, only that there are more kits. If it is the admix calculators you are asking about, then these do get updated occasionally. I am not sure what you mean about your coment about the MDLP

  7. Hi, your blog has great information. I recently tested and I am confused by my results. I am from USA and grew up in a single parent home where adoption also took place in previous generations. I knew my one parent said we had some american indian cuz we are rolled with a tribe. I am a tribal member too, Muskogee Creek Nation. I knew we had some sicilian.

    Ancestry Results
    36 Great Britain
    25 Scandinavian
    13 italy/ greece
    10 spain/portugal
    5 Irish
    4 west asian
    1 native American

    K13 eurogenes gedmatch results
    North_Atlantic 40.18
    Baltic 23.50
    West_Med 16.55
    West_Asian 3.96
    East_Med 8.68
    Red_Sea 2.93
    Siberian 1.62
    Amerindian 1.80
    Northeast_African 0.79

    I don’t know what Red Sea dna is so I googled it and found Eritrean which use to be a part of Ethiopia. Is this correct? Is siberian just part of my native American heritage? I’m assuming west med represents Spain, Portugal and East med reps my Italy/ Greece (Sicilian). For the most part the results were similar. I was told my father was German and Irish but I’m not seeing any German. I was surprised to be so much British and Scandinavian. Is it possible that there is German mixed in with my British or scandanavian? Where did the west asian, red sea, and little ne african come from? Is it from the history of different tribes taking over regions so some people are mixed up or do I have direct lineage to these asian, african regions? Why is Spain considered a country in both Europe and Africa?

  8. Determining your ancestry composition from DNA testing is still in its infancy so understand that everyone predicts a little differently.
    There is no “German” DNA. North Germans look Scandinavian (also perhaps British), southern Germans look Italian, eastern Germans look east European, western Germans look French . Germany was a crossroads.
    Yes Siberian and East Asian can be Native American
    The traces of others just show that there was more mingling in Europe than people realize…
    Read this http://blog.kittycooper.com/2016/04/ancestry-composition-comparisons-a-case-study/

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