Have you seen how Kitty Cooper’s chromosome map works with GEDmatch’s Genesis?

+14 votes
310 views
in The Tree House by Peter Roberts G2G6 Pilot (470k points)
edited by Peter Roberts
Please everyone be aware that the current version isn’t displaying triangulated segments!

That means that a lot of your nice, little matching segments are actually not proper matches at all. They are constructed (stitched) together by the algorithm of the DNA testing company during sequencing.

Please keep this in mind when you work with it, without triangulation you can’t tell which one is a correct match (meaning it’s an ancestral segment inherited from a common ancestor) or which one is random.

Don’t waste your precious time and wait until Kitty & GEDmatch have implemented it with triangulated segments.

Andreas, just a question because I'm uncertain about some things. I was unaware that any of the testing companies that allow the download of raw DNA data supply anything but the actual SNP values as digitized by the Illumina iScan system...whichever BeadChip version is in use and whatever custom programming is allowed (e.g., the GSA chip allows for up to 50,000 lab-configured bead types). The sequencing is established by the Illumina hardware, microarrays, and HTS workflow. At the end of that workflow, after enzymatic extension, fluorescent staining, and imaging on the iScan, Illumina software automatically performs some analysis and genotyping for quality control. But the raw data comes out the same regardless of the direct-to-consumer company selling and running the test, doesn't it?

In other words, as examples, the "stitching" imputation that MyHeritage does and Ancestry's use of "Underdog" genotyped phasing and "Timber" match-filtering algorithms are all applied computationally to the raw data, but don't alter the raw data itself? I know that last genotyping step that Illumina performs involves imputation for low-frequency and common minor allele variants, but I believe that's beyond the control of the testing companies.

Doesn't that mean--since the raw data is being uploaded to and used in GEDmatch, which does no stitching or imputation (I can't count things like SNP mismatch bunching limits or SNP density or the correlations necessary to align the differing versions of the human genome reference maps)--that what we see on GEDmatch is completely unaffected by whatever algorithms the testing companies choose to apply to the data after sequencing for their own reporting purposes?

And I agree with you about the value of triangulated segments, certainly beyond around 2C1R or 3C. But I think Kitty agrees with you also. She even said that functionality was almost ready. Meanwhile, I don't see that Kitty's new utility has any less value than any other "in common with" tool out there, and I believe it adds additional functionality to GEDmatch. I applaud her for it.

5 Answers

+9 votes
Awesome work. Kitty Cooper!  Thanks for sharing it, Peter.
by Carolyn Martin G2G6 Pilot (136k points)
+9 votes

You betcha, Peter! Thanks for posting this. Great minds think alike.  wink  I was excited enough about Kitty's announcement that I highlighted it this morning:

TheTribune.news

I'd followed her previous posts regarding her segment mapper, but had no idea she was talking to Curtis or John about adding it to GEDmatch. I only fired it up briefly this morning, but will make time in the next day or two to experiment.

What's maybe even more exciting is that Kitty says she almost ready with version 2.0--or at least an augmentation to the current version--that will "include everyone's match to everyone else." The much-needed function that takes us from one-to-many to each-to-each for segment triangulation. Caveat: I can't tell for certain if that capability would be a Tier 1 feature and/or if it would be tied in as a visualization option to the current triangulation utility. But I'm personally happy with however it's implemented.

We're all pretty sure AncestryDNA has no intent of upping its game for online tools, but wouldn't it be nice if FTDNA took notice that Kitty was able to write this in her home office while making lunch? Wouldn't it be great if FTDNA would give us a true each-to-each chromosome comparison utility?

by Edison Williams G2G6 Pilot (190k points)
+6 votes
Yes I have and Kitty Cooper has done it again.  Excellent work!!!
by Ken Parman G2G6 Mach 2 (28.5k points)
+5 votes
Good tool. I wish it could display more than 40 matches.

Shameless plug: I also created a Chromosome Browser to display all my ftdna, myheritage, 23andme, gedmatch matches.

Try it: https://yulvil.github.io/chromosome-browser.html

Instructions: https://github.com/yulvil/chromosome-browser
by PB Côté G2G3 (3.2k points)
This is great. Thank you for sharing. Very easy to do if you have a a basic knowledge of chromosome matching and 'dragging' and 'dropping' etc

 I have had a problem transferring MyHeritage matches over though and I haven't been able to save my work.
+2 votes
I've tried a couple different times to use this, but the boxes that are supposed to be to the right of the kit # aren't there to be able to tick them.  Anyone else having this problem?
by Darlene Athey-Hill G2G6 Pilot (277k points)

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