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ALERT – Bug in the GEDmatch “Are Your Parents Related Tool”

Dec12

UPDATE: 13-Dec-2020: FIXED! The code had not changed but the environment had, so an initialization was different. Thus my analysis that it was always the first few chromosomes helped the programmer solve the issue.

 

The “Are Your Parents Related Tool” (AYPR) has been an enormous aid to those adoptees who discover that they were a result of an in-family relationship. Thus it is very distressing to have gotten a report from a reader that the tool is suddenly showing less cM that are ROH than it used to.

My investigation has shown that the first few chromosomes have segments that are not marked as ROH when they should be and were in previous versions. The programmer who can fix this told me that this bug goes back perhaps as far as this past summer He does have a working copy from July, but is in the middle of a major new project. Thus he may not be able to attend to this until later this coming week,

In the meantime, here is an example of how this looks so you can try to make your own estimate. The results for a child of first cousins was shown in my blog post about this tool (click here for that post).

ROH for child of first cousins,  buggy version on left, previous correct version on right (click for larger version)

To the left is how that looks now, while on the right is how it looked last year. Notice that the first three chromosomes on the left have not been included in the ROH listing. Also, the previous total was 215.3 which, when multiplied by 4, fit the first cousin scenario, now confirmed. The total without those first few chromosomes today is 126.8.

The cases from closer relations are even further off. A child of siblings had 744cM ROH last year but now gets only 465.6. A child from a father daughter pairing was was 750.4 and is now 547.9. In both cases the problem was the first four or five chromosomes were not having their ROH segments counted any more.

I will post an update on this blog post once the issue is fixed.

Tool to find common ancestors at GEDmatch

Jul4

Whenever I get a new good-sized DNA match, I try and figure out how we are related. Ancestry and MyHeritage both have clever tools that search your tree and the trees of other users to come up with the likely relationship. Of course both you and your match have to have a family tree connected to your DNA on those sites for that to work.

My father’s DNA matches with matching ancestors, first run

GEDmatch has just released a tool for its Tier 1 (paid) members that will search for the common ancestor you have with your DNA matches on that site. This capability requires both you and your match to have uploaded a GEDCOM to GEDmatch and associated it with your kit. I just updated my 2015 blog post about using GEDCOMs at GEDmatch which explains much about them, so click here to read it. By the way, a GEDCOM is a text file that is formatted especially for genealogy programs; it lets you move the facts in your tree from one genealogy web site or program to another.

The new tool found nothing on my mother’s side. She was German and half Jewish. There are almost no Germans at GEDmatch and my one known half 2nd cousin on there has no tree uploaded. As to the Jewish side, very few have their trees far enough back to meet mine. I need to get a few of my known 3rd cousins to upload GEDCOMs.

The above listing, partially repeated below,  shows all the common ancestors my first run of this tool found for my Norwegian-American father using the default settings on the form. I have cut off the first 3 columns on the left which have the kit number, match name, and email address for privacy; also that makes the image readable on this page!


Let’s look at the rest of the columns for my Dad’s top match. Clicking the tree icon would take you to the user profile information. The cM shared are listed next; 40.3 is match that can be anything from a 4th to an 8th or even more distant cousin. Then the name of the possible shared ancestor, first in my GEDCOM and then in my match’s GEDCOM; either one can be clicked on to go to that person’s tree entry. The 8G is how many steps down from that ancestor my Dad is. If you click that, you see a descendant list from that ancestor in your tree. Notice that his match is also 8 steps down, so in the same generation. Subtract one to get the cousin level so this is a 7th cousin.
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Please Help Get More Kits Opted In

Feb18

I was heartbroken to learn that only about 200,000 of the more than a million kits at GEDmatch have opted in to helping law enforcement (LE). This means that most of the cases that were solved before the opt in requirement went into effect last year could not be solved today.


Dear reader, I am asking you to review the kits you have at GEDmatch and contact any cousins of yours who are not yet helping law enforcement. You might also ask relatives whose kits you do not manage if they are opted in. If you know of deceased relatives who would help if they could, send their obituary and kit number to support (there is now a form for that!) to opt them in.

Here is the email I am sending to all my hesitant cousins tonight and to many of my one-to-many matches whom I had been in touch with before. Feel free to use any of all of it in your own messages. [UPDATE: I have been accused of being too manipulative in the message below. Probably true, apologies to those I offended, but I do feel very strongly about this issue. Please reach out to your matches and relatives who have not opted in and use whatever words you prefer.]

Dear cousin —–,

I am writing to ask a favor of you. I am asking you to be a responsible citizen and bravely opt in to allowing law enforcement (LE) to compare the DNA of victims and criminals to your DNA kit at GEDmatch.com.  LE cannot see your actual DNA, only the parts that match, if there are any, to the person they are looking for. Since I manage your kit, I only need you to respond yes to this message and I will take care of it for you.

[replace that sentance with this one when you do not manage their kit]

To opt in you need to log into GEDmatch, accept the new terms, and then click the police icon next to your kit number; here is a blog post explaining how https://blog.kittycooper.com/2019/05/please-opt-in-at-gedmatch/ (towards the bottom).

It broke my heart to learn that cases like finding the killer of Tanya Van Cuylenborg and Jay Cook, solving the identities of Jane and John Does (unknown deceased victims), or clearing a falsely imprisoned man like Christopher Tapp would probably not happen today because not enough people have opted in at GEDmatch  (click any underlined words to read more about those cases).

The rules have changed so that informed consent is needed before law enforcement (LE) can compare the DNA kits of victims or criminals to yours to see if they are related to you. If they are, the tools of genetic genealogy can be used to triangulate the pedigrees to identify the family of the person of interest. This is only treated as a tip. The actual DNA of the suspect is then collected by LE from their discarded trash and compared to the crime scene DNA. [UPDATED:] Your DNA test usually remains anonymous in this process.

If you have any family members who are violent criminals, do you really want to protect them? This consent is only for violent crimes: perpetrators and victims. Please say yes, and thank you again so very much for testing your DNA which has enhanced my family research enormously.

Love cousin Kitty

UPDATE: I did not make it clear in the above post that you need to click the police icon in your list of DNA kits to opt in to let law enforcement compare their kits to yours.

So if your kit listing in the left column looks like this, click the word POLICE if you want to opt in:

One further point is that you can look up the kits of your relatives in the DNA File Diagnostic Utility to check if they have opted in. If they have not, no browbeating please, gentle persuasion or accept their decision…

Important Changes at GEDmatch

Dec17

If you have not logged into GEDmatch recently, please do so and either accept the new terms and conditions or don’t. Unless you are clearly USA based*, your kits will not be visible to your relatives any more unless you accept. I have linked to numerous other blogs at the end of this article to help you make your choice. I recommend reading either the one from Roberta Estes or EU users, the one from Debbie Kennett. Both look carefully at the new terms and conditions which are not very different from before.

Frankly, I was surprised by the panic expressed last week by some in the genetic genealogy world on FaceBook due to the sale of our beloved GEDmatch DNA tools site to a forensic science company. Personally, I hate knee jerk reactions so I did some research into this company, Verogen, as well as communicated extensively with Curtis Rodgers, one of the GEDmatch founders, and Kim Mohr, a spokesperson for Verogen.

To remind you all, GEDmatch is the best place to compare DNA tests done at different companies to each other or just to see the actual chromosome locations shared by two Ancestry testers. While both Family Tree DNA (ftDNA) and MyHeritage accept uploads of tests from other companies so you can compare on those sites, neither has the extensive tools of GEDmatch. FtDNA compares down to very small segments which can be useful in a family project but leads to inaccurate relationship estimates. MyHeritage does not show the X chromosome and neither company shows the fully identical segments (FIRs) that full siblings will have, which can be so helpful (click here).

The DNA Applications menu at GEDmatch

GEDmatch has many useful additional tools, such as “People who match both or 1 of 2 kits ,” an “Are your parents related?” test, the ability to see who matches you on a specific segment, being able to check for full siblings rather than half, and automated triangulation, to name a few of my favorites (click those words to go to that post when I did one or click here for my more general GEDmatch articles). Plus it has GEDCOM comparison utilities. Compare yours to all the ones in the database or to just one other.

GEDmatch became a center of controversy when it was discovered that genetic genealogist Barbara Rae-Venter, working with law enforcement (LE). had solved the Golden State Killer case (click here) using that site. Since that time, there have been more controversies around law enforcement’s use of the site and many overblown scare articles in the press. Personally if my DNA outs a distant cousin who is a murderer or rapist, that’s fine with me. Genetic genealogy techniques are used as a tip; no one is arrested without getting their DNA from discarded materials and seeing if it is a match to the crime scene. I know some people are afraid of the possibility of false arrests, but that just does not happen with these modern techniques. You can, as before, choose to opt out of allowing LE to see your results on GEDmatch when looking for cousin matches to the dna of the perp or the unidentified victim.

In recent months, there have been more problems, news stories and controversies, including a Florida search warrant being granted. One has to feel for the two retired hobbyists who founded GEDmatch to help in their research and ultimately help us all, keeping most of the features free. Clearly getting the site owned and managed by a more professional group would be of great advantage to the users. Curtis spent several months looking for the right partner that would respect the original misson of GEDmatch and yet deal appropriately with LE, the EU, and security issues. He and the programmers, the two Johns, will continue to work on the site as consultants.

So who or what is Verogen? Two years ago this company was spun off from Illumina (the maker of the chips and machines that all the consumer oriented DNA testing companies use to sequence your DNA). It has 50 plus employees and plans to continue growing. Their office is in a small office park near UCSD here in San Diego. Continue reading →

Please Opt In at GEDmatch

May25

In these modern divisive times, even the genetic genealogy community has been torn into two camps. Is it modern nature to react with emotion rather than thought? With the “are you with us or them”? Is this what overuse of social media has done to us? I can see both sides of the issue. Some of you may wonder what I am even talking about ….

Cece Moore on Dr Phil explaining how she uses DNA to find criminals (click image to go to that site for the article and video)

The problem has arisen because Law Enforcement (LE) has been using DNA and genealogy databases to help find violent criminals and to resolve many old and cold cases like the Golden State Killer (GSK) case. They are using the techniques and tools that were developed for breaking genealogical brick walls and helping adoptees find their biological families. Personally, I applaud this usage and the closure it brings to the families of the victims. A dear 4th cousin of mine lived in fear during her adolescent years in Sacramento because of the GSK.

However the issues of concern for many genealogists are privacy and consent. Frankly, I think you should not test your DNA if privacy is a worry of yours. So many people have tested now that you can be easily identified if you do it too. My son and two nephews have chosen not test for that reason.

How about consent? Consider the site GEDmatch.com, which was developed to let people compare their DNA tests with testers from other companies, as well as provide many helpful additional tools. If you uploaded your DNA there in the past, had you given your consent for this usage? After the GSK case. I marked all the kits I control as research until each person had responded with permission to open it up. Most were happy with the thought that their DNA might out a distant cousin who was a criminal. Polls show that 90% of Americans are OK with this too.

I have been asking everyone again since GEDmatch now has an specific opt in on each kit for LE usage of those test results in comparisons. There is also an opt in for whether the link to your WIKItree compact tree should show. Both are important. Until many more people have opted in, the benefit of the database for LE is very limited.

Why the opt in now? Why is the genetic genealogy community so divided? What happened?
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