Manual AutoClusters for LivingDNA

When I recently noticed that I had some matches at LivingDNA I did a Leeds1 analysis to analyze my shared matches to identify clusters. Now Genetic Affairs has a manual AutoCluster for LivingDNA that I can run using the CSV file that I made in my spreadsheet for my Leeds analysis. All I needed to do was to generate a second CSV file that contained my shared matches information.

To run manual AutoCluster for LivingDNA, I started with my match list from LivingDNA, shown in figure 1. I had put the name2 in Column A and the cM values in Column B, as shown in figure 2, when I ran my Leeds analysis. 

Figure 1. My list of matches from LivingDNA.

Now I added notes in Column C to my known matches because these notes will show up with my AutoCluster analysis. Both column B and C are optional, so it even works if you only supply the DNA match names. Then I saved the file as a CSV file.

Figure 2. Match file for manual AutoCluster for LivingDNA analysis.

The second file the manual AutoCluster analysis requires is a CSV file containing the shared matches. The first column of this file holds the match and the second column contains the shared match. One of the easiest ways to do get this information is to ‘view profile’ of each LivingDNA match, as shown in figure 3. 

Figure 3. View profile for an individual match.

Then scroll to the bottom of the shared matches page, highlight the entire page and copy its contents. Alternatively, you can select each shared match individually and paste it in the spreadsheet. The shared matches image from LivingDNA is shown in figure 4.

Figure 4. Highlighted shared matches for Van from LivingDNA.

Next paste the shared match information into a text editor such as Notepad on Windows or TextEdit on Mac. I’m using a Mac so the image in figure 5 is from Mac TextEdit. 

Figure 5. The copied shared matches in TextEdit.

The Mac TextEdit preserved the formatting from LivingDNA, however when I copied the names into my spreadsheet and saved as a CSV file, all the formatting disappeared and the file only contained text.  If you are using Notepad on Windows the formatting disappears when you copy it into Notepad.  Figure 6 shows my spreadsheet with the match’s name in Column A and the shared matches in Column B.

Figure 6. Shared match file for manual Auto-Cluster analysis.

The shared match file was also saved as CSV file.  I was using Excel to make these but any spreadsheet program, such as Notepad on Mac or Google spreadsheet, can be used. in order for manual Genetic Affairs AutoCluster recognizes the files, the word ‘shared’ needs to appear in the shared matches filename.  Other than that any filenames can be used.  

Next I put my data into Genetic Affairs for manual AutoCluster analysis, the URL of this analysis is: https://members.geneticaffairs.com/autocluster   Figure 7 shows the setup page.

Figure 7. Genetic Affairs manual AutoCluster entry page.

My closest match on LivingDNA is one of my Irish cousins who shares 59 cM with me.  So I the AutoCluster from max 60 cM down to 9 cM.

The AutoCluster results are sent as a zip file to your email.  First save the zip file to your computer and then unzip it.  It contains an html file with the auto cluster and an Excel file.  Figure 8 shows the auto clusters for my 60-9 cM manual AutoCluster for LivingDNA analysis.

Figure  8. Results for my 60 to 9 cM manual AutoCluster for LivingDNA.

I noticed there are some grey squares associated with the large purple cluster. Unfortunately I don’t know any of the matches in that cluster. This looks like a great opportunity to contact some of the matches there and try and find the connection. Three of my great grandparents on my Dad’s side came from Ireland, and many of my matches on LivingDNA are from Ireland or Great Britain, so they likely match me somewhere on my Dad’s side. All of my Mom’s family came from Germany. For more details on analyzing grey squares see What are Grey squares

Looking at the cluster table below my AutoCluster I can see the notes that I added for my known cousins.  The cluster table is shown in Figure 9. I’ve chatted with Mike several times and know that he matches both my Dad’s mother’s and father’s sides of my family. Harry only matches on my Dad’s father’s side.

Figure 9. Part of the cluster table from my 60-9 cM AutoCluster analysis showing the notes I added to known cousins.

A manual AutoCluster for LivingDNA analysis costs 25 credits. When you first sign up for Genetic Affairs you receive 200 free credits which allows you to run several analyses. When you decide to purchase more credits each credit costs $0.01 in US dollars. So 25 credits costs $0.25 in US dollars.

Summary

I’ve found that by generating an addition CSV file of my shared matches when I’m doing a Leeds analysis, I can now run a manual AutoCluster for my LivingDNA data. The AutoCluster gives a different visualization than my initial Leeds analysis.

Footnotes

  1. https://www.danaleeds.com/dna-color-clustering-the-leeds-method-for-easily-visualizing-matches/
  2. All names are changed for privacy reasons.

Posted in DNA

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