The formatting of the blog posting may be odd if you are reading this in a Feed Reader or via e-mail distribution, so click on the title above (which is an active link) to view the website version.
Those of us who are heavy users of GEDmatch are sorely missing the wonderful segment triangulation tool, which hasn't yet been restored since the relocation of GEDmatch to new servers. In order to be able to continue identifying triangulated groups with DNA matches, I'm using a workaround, by expanding what I previously did for the X-chromosome (Chr 23 in the figure below), which isn't included in the segment triangulation tool. In addition, segment triangulation on GEDmatch is limited to the highest 200 matches, so this method can also be used for lower level matches, even when the segment triangulation tool is back.
Figure 1: Segment Triangulation using GEDmatch Chromosome Browser
|
Steps:
|
Figure 2: DNA Matches on "One-to-Many"
|
- I then SAVE the resulting Chromosome Segment Matching webpage, so I can access it at any time, in part so I don't have to repeat the same 200 clicks, but in part so I can access it even when GEDmatch is unavailable (or when I'm off-line). To do this, press Ctrl + S (for Windows) or Command + S (for MacOS), or File then Save on the browser menu. The default filename would be “chrom_match_4c.php.htm”, but I change this and include the kit number and, for example, "Matches 1-200", the latter because I may repeat the whole procedure for Matches 201-400, 401-600, etc. In addition to the htm file, a folder with the same name and containing 23 gif files (one for each chromosome) will also be saved. You can go back and use the htm file at any time, even when GEDmatch is “down” – just click on the htm file and it will open in your default browser.
- Scroll down the chromosome plots, looking for potential triangulated groups (TGs) – for example at the black arrow in Figure 1, which shows a potential TG on the X-chromosome (Chr 23) of segments >10 cM. Make a note of the kit numbers of the individuals in this group (Lines 8-12 in the example shown – these Match IDs are found in the table above each chromosome segment plot) and the approximate location of this group on the chromosome (~18.4-28.6 Mb in this example – table not shown). Using "one-to-one" (or X one-to-one, if applicable, as in this example), compare each member of the group with the others in the group, and either include or exclude the individual from the TG, as appropriate.
X-Chromosome Segment Triangulation
Even with GEDmatch's segment triangulation tool, this does not include the X-chromosome. If I'm only interested in doing X-chromosome segment triangulation, I firstly change the order of my matches in Figure 2, sorting on largest cM in the last X-DNA column, so the X-chromosome matches are grouped together. To do this, click on the little blue triangle shown by the blue arrow in Figure 2, which will turn red once sorted, then click on boxes shown at Figure 2, #1 for anyone with X-chromosome matches. As above, click on Chr-Browse – everything can be ignored for Chromosomes 1-22, so just go down to "Chromosome 23" at the bottom, to assess the X-chromosome, then start triangulating.
Final Comments:
- Yes, this method is a bit tedious compared with using GEDmatch's segment triangulation tool, but I have found it useful during these months when the tool hasn't been available, and it is my Number 1 method for the X-chromosome (I manage far too many kits to have time to create and maintain GEDmatch segment spreadsheets for everyone).
- If you haven't ever made a donation to GEDmatch, or you haven't made one recently, please consider doing so, to help support the costs for additional servers and to minimize the chances of outages in the future. THANK YOU! There's a Paypal Donate icon at the foot of the GEDmatch Home page once you've logged in, allowing one-off or recurring (monthly) payments.
