Tuesday, January 5, 2016

How to get YDNA haplogroup from AncestryDNA results

I recently learned a fun little secret about AncestryDNA tests: their tests include YDNA SNPs!  It doesn't include as many SNPs as the 23andme test (885 vs 2000), but its often enough to provide men with their YDNA haplogroup.  Ancestry's kit is less than half the price of a 23andme kit (currently on sale for $79 with free shipping via Amazon.com vs. $199 for 23andme) so its a very economical method for getting this information.

AncestryDNA hides the YDNA deep within the raw data, so you have to do some digging to find the haplogroup.  I wanted to make this an easier process the average genealogist could do.  Here's a guide on how to get that information.

Getting a YDNA  Haplogroup from AncestryDNA Results

UPDATE #1 1/6/2015: I've updated this post with a new method that uses Felix Immanuel's tools over at y-str.org and is much more automated. However, it does not use the latest version of the Y-Tree to determine SNPs (it uses 2014 version) and might have some outdated results.  Its still best to check against the ISOGG Y-DNA Tree in case of changes.

UPDATE #2 1/7/2015: I've also added a script that will automatically reformat AncestryDNA.txt to a format compatible with the 23andme to Y-SNP Converter (special thanks to redditor /u/highlandnilo).  Your computer may give a virus warning when downloading it due to it being a VBS script.  If this causes problems you can always follow the instructions for modifying the file yourself.

Note: YDNA data is only available for male test takers.


Method One: Automated SNP extraction


Step One: Download your raw data.

On the DNA Home Page, click on "Settings" on the right side of the page.  On the settings page you'll see a box on the right titled "Actions."  The first option is "Download your raw DNA data."  Click the button just below this that says "Get Started."  You'll be prompted to enter your password.  After this, an email with a special link will be sent to your account's email address.  It may take a few hours for this email to arrive.  When it does, click the link and log in to your account.  You'll then be able to download your test results.  The result is a very large text file called "AncestryDNA."  Save this to your computer.

Step Two: Reformat the file

The program we are going to use is designed for 23andme results, so we'll need to reformat the file a bit before it will accept the AncestryDNA file as a valid input. Here is a simple VBS script that will do the reformatting for you:

Download DNAConverter.vbs.

Just download that and place it in the same directory as your AncestryDNA.txt.  Double click the script and it will create a new file called AncestryDNA_Edited.txt.  Now proceed to Step Three.

If you are unable to use the above VBS script, you can make the changes manually in a spreadsheet program.  First, open up the AncestryDNA.txt file in Excel or your spreadsheet program of choice.  You'll want to import it as a tab-deliminated file.  Next we'll need to make the following four changes:
1) Remove the header - this is the first 16 lines, all starting with a #.  Delete these rows so the table headers are the first row.
2) Delete the entire Column E ("allele2").
3) Change "allele1" to "genotype"
4) Replace all mentions of Chromosome "24" with "Y".  In Excel you can quickly do this by doing CTRL-F, going to the "Replace" tab, then putting 24 in as the text to find and Y as the text to replace it with.  Important: Also click the options button and select "Match entire cell contents."  The click "Replace All"
When finished, save this edited file as a txt file.  Do not worry about any compatibility warnings Excel might give you when saving.  

Step Three: Download Felix Immanuel's 23andMe to Y-SNP Converter


Felix Immanuel's Y-STR.org site has a ton of great tools for in-depth analysis of DNA results.  This particular tool parses the data of a 23andme raw data file and outputs YDNA SNPs.  In the last step, we converted our AncestryDNA file to the proper format for this program to read.


Run the program and select the edited AncestryDNA file you created in the prior step.  It will output a list of YSNPs:
Now go to File > Save Y-SNPs.  This will create a text file called YSNPS.txt

Step Four: Obtain your Haplogroup

Now go to Chris Morley's Y-SNP Subclade predictor website.  Copy the contents of the YSNPS.txt file into the box on that page and click Predict.  Your possible Haplogroups will be displayed on the left.  It should look something like this:

You may have to select the second or third choice to find your correct haplogroup.  It will be the one with the most green in it.  However, you should IGNORE root ancestral groups such as BT or F.  If BT or F is your most likely group, proceed to the next one on the list with the most green. 





Method Two: Promethease


Step One: Download your raw data.

On the DNA Home Page, click on "Settings" on the right side of the page.  On the settings page you'll see a box on the right titled "Actions."  The first option is "Download your raw DNA data."  Click the button just below this that says "Get Started."  You'll be prompted to enter your password.  After this, an email with a special link will be sent to your account's email address.  It may take a few hours for this email to arrive.  When it does, click the link and log in to your account.  You'll then be able to download your test results.  The result is a very large text file called "AncestryDNA."  Save this to your computer.

Step Two: Obtaining the YDNA data.


To obtain your haplogroup, you'll need to run the raw data file through Promethease.com.  This service reads your DNA test results and outputs a health report, all for the very low cost of $5 (there's also a slower free version available here).  Simply upload the file you received from AncestryDNA to the Promethease website and it will provide you a health report.  Just remember to save the report to your computer after you run it, as it will expire after 30 days!

Promethease reports categorize your results based on different medical or information topics.  To find the haplogroup info, click on the "Topics" drop-down menu on the right side and select "Haplogroups."  Next, select the drop-down that says "Sort by magnitude" and change this to "Sort by frequency."

Want to see what a Promethease report looks like before you buy it?  Try the above search on this example report.

Step Three: Interpreting the results.


You're now looking at a list of YDNA SNPs known to indicate a person's haplogroup.  The top results will be the rarest, and most likely to indicate the terminal haplogroup.  Unfortunately the information provided by Promethease doesn't go into detail on what each YDNA marker means.  So we'll have to look at a second website to interpret the results.  In a separate browser window, open up the ISOGG YDNA SNP Index.   Now highlight the RefSNP ID (aka "rs" number) of the top (rarest) result in Promethease.  On the ISOGG page, do a CTRL-F search and paste in the rs number.  Hopefully it will be in this database and jump to the correct SNP.

On the ISOGG page, each SNP entry will have something in the rightmost column like "A->T" or "G->A".  This is the change that indicates whether or not someone is positive for that particular haplogroup.  The letter on the left is the ancestral version.  The letter on the right is the mutation that signals your test belongs in that haplogroup. You'll want to compare this to your Promethease results to see if you are positive or negative for each haplogroup indicator.

So for example, if my top Promethease result for haplogroups is "rs17250535(A;A)" then I  will search for "rs17250535" on the ISOGG page.  I then see the mutation for this SNP is T->A.  Since my result in Promethease was (A;A), I am positive for this mutation and belong to this haplogroup, which the ISOGG page reveals is R1a.  Had I been negative (T;T), then I would have proceeded to the next SNP in Promethease.  Its a good idea to try a few of the SNPs, just to be sure.  Keep in mind that if you fall in a subgroup like R1a, you should be positive for all parent groups as well, such as R1 and R.

Promethease does not provide a complete listing of relevant YDNA SNPs.  But typically it will provide enough for you to discover the rough haplogroup.  Once you've found your group, it might be a good idea to search for more SNPs relevant to that particular group in your raw data from AncestryDNA.  Admittedly its not the easiest process, but its cheaper than any of the other options for obtaining YNDA results.

134 comments:

  1. Thanks for the description on how to get this detail. You have given a ton of food for thought, and I now find that I want to take some entry level DNA courses so I can understand what the heck I am looking at. Have done 3 sets of Ancestry DNA (Male=me, Female=eldest sister, and Female=wife (alas no living direct males). I have a ton of detail, now to interpret what it all means and why.

    ReplyDelete
    Replies
    1. You can get the basics of terminology and methods at this page: https://sites.google.com/site/wheatonsurname/beginners-guide-to-genetic-genealogy
      I'll be adding some guides for using AncestryDNA in the future.

      Delete
    2. Updated with an easier, automated method! No more searching the ISOGG tree.

      Delete
    3. Steven Frank, I tried your program and got as far as Chris Morley Haplotype predictor. I have tried repeatedly to get it to accept my "Y SNP" data, but it wont. Here's what the fisrt few lines of the Y data look like.Y-SNP Derived RSID Chromosome Position Genotype
      M176/Page63/PAGES00063/SRY465/PAGE063 No rs11575897 Y 2655180 G
      Page65.1/PAGES00065.1/SRY10831.1/SRY1532.1/SRY10831/PF6234 Yes rs2534636 Y 2657176 C
      S27649 No rs35840667 Y 2661306 T
      L311/S4144 No rs2253109 Y 2661694 G
      S27626 No rs35067692 Y 2663685 T

      I put that in, it doesn't recognize the M176... I try with another of my SNP's, same thing. I try different formats, same thing. Did I mess up?

      Delete
    4. Steven Frank, I tried your program and got as far as Chris Morley Haplotype predictor. I have tried repeatedly to get it to accept my "Y SNP" data, but it wont. Here's what the fisrt few lines of the Y data look like.Y-SNP Derived RSID Chromosome Position Genotype
      M176/Page63/PAGES00063/SRY465/PAGE063 No rs11575897 Y 2655180 G
      Page65.1/PAGES00065.1/SRY10831.1/SRY1532.1/SRY10831/PF6234 Yes rs2534636 Y 2657176 C
      S27649 No rs35840667 Y 2661306 T
      L311/S4144 No rs2253109 Y 2661694 G
      S27626 No rs35067692 Y 2663685 T

      I put that in, it doesn't recognize the M176... I try with another of my SNP's, same thing. I try different formats, same thing. Did I mess up?

      Delete
    5. You are not using the correct Save option. Use the third in the drop down, File > Save Y-SNPs then open the file and copy the text within and paste it into the dialogue on the Chris Morley Haplotype predictor. Hope that helps. Mel

      Delete
    6. Hello. I read your FB ad today. Just want to let you know in case you don't, that PROMETHASE.COM is FOR SALE. Try as I may I cannot get past their for sale sign. So I'm assuming they are not accepting and new DNA test results from other sites.

      Delete
    7. Sheilarena - The site is https://www.promethease.com/ which is not for sale.

      Delete
  2. I've spent several hours attempting to get a file Felix Immanuel's 23andMe to Y-SNP Converter will accept. Question 1) is there a column width restriction? 2) is the text right or left justified and 3) is there a file format restriction?

    ReplyDelete
    Replies
    1. The file is a tab delimited spreadsheet. You shouldn't need to reformat it in any way other than those four changes. When you make the changes, just save it back to a text file, not as an excel file as that won't work. Excel may give some warning about incompatibility, just ignore that.

      I'm working on a version that will automate the reformatting of the file, as you're not the only one having this issue.

      Delete
    2. Thank you for the reply. I'll wait for an update.
      Cheers,
      Debbie

      Delete
    3. I've updated the process with an automatic option! Try it now and let me know if you have any problems.

      Delete
  3. I got mixed results ... what next?

    Method 1: BT-M139 (BT-M42, BT-M94)


    Method 2:
    rs17250535 A A Y 21311315 RBMY2SP R1a
    rs9785659 G G Y 16136818 R1b1a2a1a

    Thanks!


    ReplyDelete
    Replies
    1. BT isn't a modern haplogroup. The webpage oftens lists that as the top one because it is something everyone matches, when in actuality your haplogroup will be one under it. Try the next few on the list until you see one with lots of green. Its probably the second or third on the list. It still takes a little discernment, but a lot less than method.

      Delete
  4. Will this work if the person was tested at Relative Genetics and their results were transferred to Ancestry?

    ReplyDelete
    Replies
    1. I believe the Sorenson/Relative Genetics test was a Y-STR test, not a Y-SNP test. I'm not familiar with how the results look now in Ancestry, but if you have the Y-STR values it tested, you can put them in a Y-STR calculator and get your haplogroup prediction. Here's one to try:http://www.hprg.com/hapest5/

      Delete
  5. Could you make a youtube video of how to do this? I learn better by a visual aid.

    ReplyDelete
  6. Wow this is amazing and it works really well!

    ReplyDelete
  7. My computer will not open the DNA Converter.vbs. When I try the second option of exporting AncestryDNA.txt to Excel it states the file is corrupt can cannot be imported to excel. What do you recommend now?

    ReplyDelete
    Replies
    1. Try opening the AncestryDNA.txt file in Google Sheets: https://docs.google.com/spreadsheets/u/0/ Click the little folder icon on the right then select upload and upload the file. If that doesn't work then your AncestryDNA.txt is indeed corrupted and you should try redownloading.

      Delete
  8. Steven: Is there any way to determine the Haplogroup from Ancestry's atDNA (Autosomal) test....or is it impossible since it contains DNA from both parents?

    Thanks!

    ReplyDelete
    Replies
    1. This method works for AncestryDNA tests so long as its a test done on a man. It will give a rough idea of his paternal ydna haplogroup.

      Delete
  9. I would say, add step 2. Unzip your the data file, because other programs use the ancestry file in its zipped state and I tried for 15 mins to get the DNA converter to work before thinking hmm. Probably should unzip it. :P

    ReplyDelete
  10. I would say, add step 2. Unzip your the data file, because other programs use the ancestry file in its zipped state and I tried for 15 mins to get the DNA converter to work before thinking hmm. Probably should unzip it. :P

    ReplyDelete
  11. I am sorry to bother you but maybe you have seen this error. Any help?
    Enter a list of SNP calls, in one of the two supported formats:
    Error: No call specified for "M176/Page63/PAGES00063/SRY465/PAGE063 No rs11575897 Y 2655180 G". Please check that the correct data format is selected (see notes below). Then check the call for "M176/Page63/PAGES00063/SRY465/PAGE063 No rs11575897 Y 2655180 G".

    M176/Page63/PAGES00063/SRY465/PAGE063 No rs11575897 Y 2655180 G
    Page65.1/PAGES00065.1/SRY10831.1/SRY1532.1/SRY10831/PF6234 Yes rs2534636 Y 2657176 C
    S27649 No rs35840667 Y 2661306 T
    L311/S4144 No rs2253109 Y 2661694 G
    S27626 No rs35067692 Y 2663685 T
    PF6399/S10 Yes rs2058276 Y 2668456 T
    S27555 No rs28813670 Y 2703038 G
    S27173 Yes rs11799203 Y 2705854 G
    Page52.3/PAGE052/L1035/PF3228 No rs34402762 Y 2710309 T
    - - rs13305196 Y 272Y13 G

    ReplyDelete
  12. I have the promoethease report and its an html. I went to topics and there are a few things that say haplogroup....
    Haplogroup I 2 snps
    Haplogroup K 2 snps
    Haplogroup R1b1b2g 3 snps
    Haplogroup Y 252 snps
    And one that just says Haplogroup

    However i can't do any sorting like you suggested

    ReplyDelete
  13. I am puzzled. I ran the procedure for both my son and his paternal uncle (father's father's brother). Both came through with DE as the Y-DNA group which seems odd. The family is Jewish, Caucasian, and emigrated from Ukraine. Yet when I googled the DE haplogroup it indicated that it has died out in Europe and is still only alive in scattered places throughout the world. Is there another test I need to do? Or am I reading the results wrong. There's only one green band on the results.

    ReplyDelete
    Replies
    1. DE is an ancestral group that no one has anymore. Sometimes the webpage predictor will return an ancestral group as the top match but the actual group is farther down. What are the next few options? Most likely they are an E haplogroup.

      Delete
    2. Thank you for your reply.
      I re-ran the predictor under isogg the second time and got the DE again, but at the bottom of the page was the R1a1 or R1a-M516 as a possible designation. The DE was still at the top, and the R1a1 was the last choice on the page. I got the same result for his great uncle. I do have an FTDNA Y-test in progress for my son and should soon have those results. It will be interesting to see how close the predictor is.
      Thank you again for your help.

      Delete
  14. Tried to download the .exe and it said it was a virus - it refused to download

    ReplyDelete
    Replies
    1. Try downloading this zipped version instead: https://goo.gl/VpSrRK

      Delete
    2. Got virus detected right before it finished downloading.

      Delete
    3. Then you'll probably need to temporarily disable the virus software to download. Some virus scanners are more sensitive than others. Also I'm not the author of the program so I can't vouch for its content other than to point out that the author, Felix Immanuel, is well-known in genetic genealogy circles and has a Masters in cyber security to boot.

      Delete
    4. Sounds good. Decided to do that and it ran fine.

      Inputted the information into that site and first one I got was BT, so ancestral.

      Second one I got was E1b1b1b2a1a with this below it:
      E-CTS1096 (E-CTS4041, E-CTS4068)

      Then E, with this below it:
      E-PF1796 (E-PF1476, E-PF1557)

      THen E1b1a1 with this:
      E-CTS3105 (E-CTS3989, E-CTS4350)

      Then G2 with this:
      G-PF3119 (G-PF2839, G-PF3125)

      Which one would be my haplogroup? Sorry for all of the questions

      Delete
    5. E1b1b1b2a1a. The reason it doesn't show up #1 is due to how few markers AncestryDNA tests.

      Delete
  15. I've tried both of these methods, and am confused about the Promethease method #2. When using method #1, my most likely haplogroup is: R1b1a2a1a ; R1b-L11 (R1b-L52, R1b-L151). Then with Promethease, my top 3 (lowest frequency) SNPS are: rs4589047(A;A) 0%, rs17250535(A;A) 3.4% and rs9785959(C;C) 31%. When I look these up on the ISOGG index, the first one rs4589047 says mutation is A->T where in my Promethease report it says (A;A) so my understanding is that is negative. Moving on to the next 2 they seem to fall under R1a, where as the method #1 conclusion was that my halpogroup falls under R1b. Any advice or clarification would be much appreciated. This is exciting stuff... thank you so much!

    ReplyDelete
    Replies
    1. I'd say R1a based on The L146+ call, but it would be interesting to see what snp's were positive in the Method #1 call for R1b. Also were there any negative (red) in the R1b call?

      Delete
    2. Yeah there are a number of negative SNPS on the Morley report, and no reference to R1a or L146+ (using ISOGG tree). With the 'Experimental' Morley tree it also seems to lean toward R1b1a2a1a.

      Here's a picture of my result from method 1 ISOGG: http://imgur.com/1h1AkrH

      Here's ISOGG Experimental tree:
      http://imgur.com/McVA9Sc

      And here's my result from method 2:
      http://imgur.com/8HkUNrQ

      I'm new to YDNA & also to Prometheus, so not all that confident I know what I'm doing yet! That said, I feel that the 1st method pointing me to R1b seems more trustworthy, and R1b seems likely based on my admixture reports and atDNA matches showing mostly European ancestry.

      I definitely hope to get a proper YDNA test done some day (maybe if prices ever drop!). Thanks for this great tutorial to help many of us get our feet wet.

      Delete
    3. It does look like the R1b prediction is pretty solid. Its sometimes possible to have an SNP mutation that is not relevant to your haplogroup. Perhaps that R1a positive was of that type

      Delete
    4. My husband's first two listings on Promethease are the same as delerivm, above: rs4589047(A:A)[A->T]at 0% *F*; and rs17250535(A:A) [T->A] at 3.4% *R1a*; then,
      rs2032624(A:A) [A->C] at 31% *R1*;
      rs17307070 (G:G) [G->T] at 31% *R1*; and,
      rs17250887(T:T) [A->T] at 31% *IJ*
      [isogg notes in brackets] Haplogroups in *x*

      Method one, extraction and conversion, however, seems pretty clearly to indicate Q1a2a1/Q-CTS11350 (Q-CTS7619, Q-L54). It's the first listed and "most green" after BT in the experimental tree; and first listed in the ISOGG tree.

      Say what? Any reading suggestions?

      Thanks for an interesting process, even if I don't understand where I could have input info incorrectly to get such divergent results.

      Peace,
      Jo

      Delete
  16. Hi,

    I have tested 2 family members. The results each show a large block of green highlighted data. Neither green ares show a clear Haplo group. I suspect I am missing something here but photos I took of results show the data in the green areas very clearly.
    Is there any further advice you can give me?

    Jenny

    ReplyDelete
  17. I really don't recommend using AncestryDNA's Y SNPs. I outlined my reasons in this post on the Ancestry board (inconsistency, derived values in females, etc.)

    http://boards.ancestry.com/topics.dnaresearch.generalresearch/772.2.1.1.1.1.1.1.2.2.2.2/mb.ashx

    ReplyDelete
  18. Thank you, this is helpful. Learning how to understand this genetic data is quite the challenge, like untangling an untidy stash of yarn, so I feel grateful to you for your contribution in untangling a few of the stands.

    Unfortunately, I can't quite get all the way there with what you've written because I don't know enough to decipher why, per your example, your A;A matches isogg's T->A. Or in my case, does my G;G match isogg's A->G? Is it that I don't know what -> means?

    Also, in isogg, rs3913, which is first in my promethease haplogroups by frequency, lists two Y-positions, both of which have A->G to the far right.

    Would you mind explaining how to understand two Y-positions and how to derive the positive/negative from the mutation, i.e., A->G?

    Even if you haven't time to explain, I appreciate your contribution very much, as well as your excellent grown-up writing skills.

    ReplyDelete
  19. BTW Only after 14(!!) attempts did my comment finally post.

    ReplyDelete
  20. Will this work for a female's Ancestry DNA?

    ReplyDelete
    Replies
    1. No, only for a male test taker's Ancestry DNA.

      Delete
  21. Hello Steven,
    Please forgive such a pedestrian question, but I've done the Prometheus. The first Haplo Group was A>T, and I understand this is negative. Going to the next rs17250535 (A;A) T>A, is positive, so the results are R1a.

    Okay, here's where I get lost. Now what? The next results is rs2032624(A;A) ISOGG is A>C. (These are my FILs ancestry results. Thanks so much for the info!)

    ReplyDelete
  22. I believe he's saying -> means a mutation confirming haplotype; where ISOGG A->G means "A" is what the upstream haplotype has at this position and "G" in this position is what defines the downstream haplotype mutation, so you are "positive" for this mutation which is a confirmation sign for the downstream haplotype.

    ReplyDelete
  23. Hi there! I am a totaly DNA noob. I have a question about my Y-SNP results using the MorleyDNA.com Y-SNP Terminal Subclade Predictor. Whatever my results are if it is showing Y information it is from my father's side, correct? Also, how is it able give me results for Y if I am a girl? I thought Y was only carried by men... Does this mean my results are incorrect or is it showing a mixture of all the Y that I carry (assuming women can carry y information... This is so confusing).

    ReplyDelete
    Replies
    1. No, you don't have any Y SNPs, but the probes in the off-the-shelf Illumina kit seem to pick up short stretches of DNA that are also found in the autosomal chromosomes. This is one of the reasons that I don't recommend using AncestryDNA's Y SNPs.

      Delete
    2. Thank you for your response. Could explain a little more about what this means? Does it mean in some way that I am seeing other male family member's (e.g. my maternal or paternal grandfather's or my dad's) Y SNPs and therefore, I am seeing other of my male relative's haplogroups? Also, which DNA test would you recommend for me to use to find my haplogroup (both Y and X)? Thank again for you help in clarifying this!

      Delete
    3. No, you are not seeing any Y DNA from your male relatives. The Y SNPs are not reliable in all cases. You have no Y haplogroup because you do not have a Y chromosome, but you can test certain male relatives to learn your father's haplogroup (your father, your brother, your paternal uncle...)

      The X chromosome is one of the nuclear chromosomes, and it does not have haplogroups. You're probably thinking of mitochondrial DNA, which you receive from your straight maternal line. You can learn that by ordering an mtDNA test from FTDNA. 23andMe will also give you a certain amount of information about your mtDNA haplogroup (more than the HVR test at FTDNA, but less than the full mitochondrial sequence).

      Delete
    4. Thank you again for clarifying! So, in order to get both my maternal and paternal haplogroups, would you suggest just getting the 23andMe test or would you suggest another?

      Delete
    5. You won't see a paternal haplogroup if *you* test at 23andMe. If you have a brother, he could get a test and get both the paternal and maternal haplogroups. Males do inherit mtDNA from their mother, but they don't pass it on to their children.

      Delete
  24. Here's the results:
    U175 E1b1a1a1d rs16980588 (A;G) 16253694 G->A
    S119 I2a2a P220 rs17316910 (G;T) 24475669 G->T
    M221 J2b rs2032667 (A;G) 15436316 G->A
    P295 P PF5866; S8 rs895530 (T;T) 7963031 T->G

    M185 L PF5755 rs2032607 (T;T) 14904859 C->T
    P150 E PF1704 rs9786893 (A;C) 16846439 C->A


    What haplogroup am I? (these are a male relative's results)

    ReplyDelete
  25. Those are incompatible haplogroup assignments, another problem frequently encountered trying to parse AncestryDNA Y SNPs. See the skeleton tree at

    https://en.wikipedia.org/wiki/Human_Y-chromosome_DNA_haplogroup

    ReplyDelete
  26. OK, here were my results using method 1:
    I1
    I1-L759 (I1-CTS10140, I1-CTS10338)

    O3a1
    O-F672 (O-F110, O-CTS5687)

    R1b1
    R1b-L506 (R1b-L278, R1b-M415)

    R1a
    R1a-F3650 (R1a-F928, R1a-CTS10627)

    None were green.

    Using the second method, my 0% was not a match, at 3.4% it said I was R, then three at 31% said I was IJ. Then after several misses one at 69% said I was R.

    If anyone can help me translate this I would appreciate it.

    John

    ReplyDelete
    Replies
    1. Now I see they are green after you select them.

      Delete
    2. DNA Cousins can you help me interpret those results? Thanks. My initial comment came up as unknown, but it was from me.

      John Stromberger

      Delete
    3. Maybe the author of this column can answer you better. My position in the comments has been that the Y-SNPs in the AncestryDNA raw data are not well suited for haplogroup labeling.

      Delete
    4. I can't help based on what you posted. Try method #1 again and see which result has the most green and least red. Ignore root haplogroups. Focus on the most specific ones.

      Delete
  27. Where can I find a converter table for Y chromosome hg 3, 9, 26 etc, etc?

    ReplyDelete
  28. Are you referring to a nomenclature system that predated the Y Chromosome Consortium's paper back in 2000? This article has a tree with different columns showing various old-style labels created by different researchers:

    http://www.ncbi.nlm.nih.gov/pmc/articles/PMC155271/

    ReplyDelete
  29. This is a GREAT resource/tool you've provided. I test family members on an ongoing basis. And since 23 has gone up on its price, AncestryDNA is the affordable route but lacks haplogroup assignments. This is an excellent alternative for my male testers. Thanks a mil!

    Karim R

    ReplyDelete
  30. Karim R, could I beg you into helping me on one male relative? I've tried numerous times, forwards, backwards and upside down standing on my head! All with zero results! akgigante@sbcglobal.net

    ReplyDelete
    Replies
    1. Hi Kathleen. I'll help you out over on facebook.

      Delete
  31. I am using a Mac and when I import the raw DNA to Numbers, it only gives me Chromosomes 1 & 2. Any help?

    ReplyDelete
    Replies
    1. I have discovered that Mac's Numbers spreadsheet is limited to 2^16 rows which only allows me to get to chrom. 2. Can I create multiple spreadsheets to be processed?

      Delete
    2. You can open your AncestryDNA download with most text editors. Copy just the rows with data for chromosome "24" (the way AncestryDNA denotes the Y) to a new file. But.. as I've mentioned above, the results can be rather flaky.

      Delete
    3. Surprisingly, there is no chromosome 24 listed!

      Delete
  32. This comment has been removed by the author.

    ReplyDelete
  33. I am a little confused about my husband's results using Method #1. His most likely haplogroup was listed as R1b1a2a1a based on positives for L11/PF6539/S127 and PF6546/P310/S129. However, he is not positive for M343/PF6242, which is the defining mutation for R1b. He is also negative for M405/S21/U106, and he is not positive for any of the other subclades under R1b. He is positive for M420/L146/PF6229, which is the defining mutation for R1a. And he is positive for PF6506, the mutation for R1a1a1b1a2b3~2§, but he is not positive for M17, the defining mutation for R1a1. I can't really decide which one is his actual haplogroup. Thank you so much for the help.

    ReplyDelete
  34. Steven,

    I'm a complete novice when it comes to DNA analysis so please could you help me with the results from Morley?
    The 'most likely result was:
    BT BT-M139 (BT-M42, BT-M94)

    The others below it are:
    J J-YSC0000239 (J-CTS3936, J-CTS1068)

    I1 I1-L759 (I1-CTS10140, I1-CTS10338)

    O3a1 O-F672 (O-F110, O-CTS5687)

    R1b1 R1b-L506 (R1b-L278, R1b-M415)

    Thanks,
    Jack

    ReplyDelete
    Replies
    1. BT is an ancestral group not found in living people Your actual haplogroup would be downstream of that. See this tree: https://en.wikipedia.org/wiki/Human_Y-chromosome_DNA_haplogroup for a visualisation. Only the haplogroups at the end of the branches are present in living populations. I wish Morley's page didn't even include BT, but that's not up to me. I've made the warning about this in the article a little more prominent.

      The option with the most green and least red after BT is the best guess. But your list there is kind of all over the map so it makes me wonder if perhaps you aren't in one of the groups that is not covered by the AncestryDNA's SNP sampling.

      Delete
    2. Steven,
      Thanks for the quick reply.
      By the 'most green and least red' assumption i cannot find an answer to that because there always seems to be more red, or in the 3rd result down (O3)there is one red and one green within the green box, same with (R1b).
      I'm really not sure what to agree with. As you say there might be a chance AncestryDNA haven't covered it.

      Jack

      Delete
    3. Jack,
      Yes, its likely ancestry doesn't have coverage for your haplogroup. Their test wasn't intended for YDNA haplogroup determination, and just happens to have some SNP coverage included. This works well for some people but not at all for others. Sounds like you fall into the later category. You'll have to do either 23andme's test or a Y-STR test from FamilytreeDNA to learn more about your Y haplogroup.

      Delete
  35. Hi Steven, I wonder if you could help me - you said ""rs17250535" on the ISOGG page. I then see the mutation for this SNP is T->A. Since my result in Promethease was (A;A), I am positive for this mutation and belong to this haplogroup, which the ISOGG page reveals is R1a." -

    However on the excel list I'm looking at it only says 'R' not R1a. Am I looking at the wrong page? I have gone through all available entries for the Y chromosome on my Dad's DNA and the only positives I have are:

    P157 F rs9786095 24359931 T->C CC
    M89 F PF2746 rs2032652 21917313 C->T TT
    PF2746 F M89 rs2032652 21917313 C->T TT
    PF2617 F P145 rs17842387 8424089 G->A AA
    PF2734 F P148 rs16980396 19349615 C->T TT
    PF3525 IJ P130; S22 rs17250887 8558969 A->T TT
    R rs9785959 17782178 C->G GG
    PF6229 RL146; M420 rs17250535 23473201 T->A AA
    M22 L rs3913 14790163 A->G GG

    And these anomalies
    PF5480 K P132 rs3853054 8679843 G->T AA
    P132 K PF5480 rs3853054 8679843 G->T AA
    M3 Q rs3894 19096363 G->A CC
    P205 DE M145; PF1444 rs3848982 21717208 C->T GG

    Promethease seems to assign these to different Haplogroups to the SNP index as well.. I thought I understood this but am not so sure now! Wishing I'd done 23andme for Dad as well as Mum now. :/

    Many thanks
    Jenny

    ReplyDelete
    Replies
    1. Its R1A. See the table here: https://www.snpedia.com/index.php/Haplogroup_R_(Y-DNA) You could maybe find some downstream SNP mutations with some very serious hunting through the data, but it might not be worth the effort.

      I tell the people at my genealogy workshop that in general I don't recommend 23andme, but if you're going to do it, do it with a male sample so you get all of your money's worth. The Y data is some of the most helpful info that test gives.

      Delete
    2. Hello - ah yes thank you I had not seen this page.
      Yes, I really think I did it the wrong way around... however I did find someone looking for their adoptive family on 23andme and my Mum was his only match (2nd cousin) so not a waste for him. Just need unlimited money to do them all! :)

      Delete
    3. Can I just ask - where do the anomalies come from? So the excel sheet said to expect GG or TT and I got AA - Is this ancestry DNA making a mistake or something different?
      Also I have more negative results for 'R' than I do positive when going through using the second method, which I think is what confused me... oh dear!
      Many thanks (again!)

      Delete
  36. I'm having trouble getting the raw data into the necessary format. My spreadsheet runs out of rows to accommodate all the data. Also, my data has no chromosome 24! It skips to chr. 25. Thanks for any help.

    ReplyDelete
    Replies
    1. Is it a woman's data? Women do not have a Y chromosome, so there is no Chromosome 24 data to work with.

      Delete
  37. No! It's my husband's DNA ! Just downloaded it again from ancestry and it's the same. I also get an error message from Google Sheets that it's too much data

    ReplyDelete
  38. I found chr. 24 on the new download. Now to get Google Sheets to work!

    ReplyDelete
  39. Another question from a neophyte: I need to process all the chromosomes to find the Haplogroup or just chromosome 24? Still having trouble getting all the data uploaded into a spreadsheet. Even Google Sheets says there's an error. Thanks! This is driving me crazy!

    ReplyDelete
  40. Hello Steven

    I was lucky enough to find your site here. I used your Method 2 on my brother's DNA.To say the least I was quit shocked by the results. My brother is showing a Haplogroup of F. I ran several rs# and of all that my brother's was positive for came back with the same haplogroup of F. Everything that I am reading says that this haplogroup is no longer used or is very old. Where should I go next in finding the actual haplogroup? Thanks for your help.

    Some of my brothers results:


    rs16980396 (C;C) SNP P148 PF2734 mutation C>T

    rs17842387 (G;G) SNP P145 PF2617 mutation G > A

    rs2032652 (C;C) SNP M89 PF2746 mutation C > T

    rs9786095 (T;T) SNP P157 mutation T > C

    ReplyDelete
  41. If you tested on Ancestry chip v2, more y SNPs are included. You can go for free onto Wegene (Wegene.com/en/), a Chinese genetics company, and they will give you both your Y and mt Haplogroup. My Y-Haplogroup is C2e1b2!

    ReplyDelete
    Replies
    1. I've been working on a spreadsheet method to get Y haplogroups from v2 SNPs. In general, the haplogroup assignment seems much broader, deeper, and more internally consistent than with v1. But I've only seen sample data from a couple of haplogroups. Would you (or anyone, for that matter) mind sending me your Y-SNPs? I'm Ann Turner, DNACousins@gmail.com.

      I've also looked at the mtDNA SNPs. The majority seem to have been selected for medical relevance. They don't even include SNPs used for a backbone test.

      Delete
  42. I'm so confused. I've put my husband's Ancestry DNA into Promethease. I have tried searching his first 5 rs numbers (obtained as per your instructions) in the ISOGG index but I"m not getting any matches. (in fact I can't actually see any rs numbers listed). I thought I had done as you explained. Do I just carry on until I get a hit or am I doing something wrong?

    ReplyDelete
  43. Feeling like a fool... Trying to use promethease on my ancestry.com raw data.

    1) I go to http://isogg.org/tree/ISOGG_YDNA_SNP_Index.html

    2) Then I click on CLICK HERE TO VIEW THE INDEX (A GOOGLE SPREADSHEET)

    3) I have my Promethease Report set to Haplogroups (116) and Sort by Frequency

    4) My top result is rs4589047(A;A) 0% Frequency. I search rs4589047. One hit. A->T. I am not a match, so I go to the next.

    5) rs17250535(A;A) 3.4% Frequency. One hit. T->A. I match. Haplogroup R. Still, I'll try another.

    6) rs9785959(C;C) 31% Frequency. One hit. C->G. Not a match. On to the next.

    7) rs17250887(T;T) 31% Frequency. Three hits. All are A->T, all matches. Haplogroup IJ. Next.

    8) rs9785659(G;G) 65.5% Frequency. Three hits. All are A->G, all matches. Haplogroup R.

    9) The rest, ending with rs17307070(T;T), all had me matching R or NOT matching IJ.

    Two questions.
    1: Why IJ that one time??
    2: Why only R, with no numbers after it? No R1a, or whatever, for me? In fact, there are no numbers in the Haplogroup
    column, other than 0 or 00 a few times.

    I can't be doing this correctly.

    ReplyDelete
    Replies
    1. OK, just learned about the 2x at the bottom of the page.

      rs9785740(G;G) 69% has two hits, both matches with A->G, Haplogroup P.

      rs2534636(C;C) 96.3% Frequency has five hits. Four are C->T/not matches. But one is T->C, a match. Haplogroup BT.

      My final one is:
      rs2032612(C;C) 100% Frequency. One hit. C->T. No match. In this case, not matching Haplogroup C.

      So it only got worse after hitting 2x!!!!!!!!

      Delete
  44. I would like to thank you for all your work that allows amateur genealogists like myself reach a whole new level of enlightenment. Never before would I have thought that a simple $99 DNA test at ancestry.com would allow me to find my haplogroup and my genetic DNA markers. For what it's worth, I am also rs17250535 (A;A) and haplogroup R1a. It will be hard to just call myself an Italian American or an American mutt. Truly inspiring. Much appreciated.

    ReplyDelete
  45. Thank you for this page. I followed the first method and it worked well. My grandfather's haplogroup is I1. Are there similar methods out there to tease out mtDNA from raw dna files?

    ReplyDelete
  46. This blog entry has been very helpful for me. I did get a result from Method 2, but have been struggling to complete Method 1. I want to convert my AncestryDNA raw txt file using your vbs script. However, I use Linux and Libreoffice/OO won't work. In an earlier comment you indicated that Google Drive would work if I opened my AncestryDNA,txt file with Google Sheets. But when I try to do this, from within Sheets, the Doc app ends up opening the file. Is there a way to force Sheets to open the txt file and run your VBS script? And can you verify that this conversion can be accomplished within Google Drive?

    ReplyDelete
    Replies
    1. I read this blog more carefully and realized that I could "manually" edit the raw AncestryDNA.txt file... I just had to follow the 4 steps to filter the data. So there is no need to use the VBS script. Every thing else went smoothly as described in this blog entry. And good news, Method 1 had the same result as Method 2. Thanks Steven!

      Delete
  47. "The top results will be the rarest, and most likely to indicate the terminal haplogroup" Does this mean top as in the first result on the Promethese results, or Top as in 100%?

    ReplyDelete
  48. Hi. When obtaining YDNA results from promethase, why does one use the rarest rs number for haplogroups?

    ReplyDelete
  49. Is there a way to manipulate the Raw Data to find Mitochondrial DNA for women??? Pretty please with a cherry on top?

    ReplyDelete
    Replies
    1. Not really. Most of the mtDNA SNPs appear to have been selected for their medical interest, and the remainder have very haphazard coverage of the SNPs used to define haplogroups.

      Delete
  50. This comment has been removed by the author.

    ReplyDelete
  51. Good afternoon Steven Frank, the reason why i am reaching out to you is because i an having a hard time and confused on trying to understanding the Promethease method #2, I am new to all of this so how can i find my Promethease result for haplogroups?

    ReplyDelete
  52. i did it by the promtheaus method and found m420 is that too broad? can i trace back more recently or is this a good enough match?

    ReplyDelete
  53. I don't know how to copy the contents of the Y-SNPS file to the box? Any help?

    ReplyDelete
  54. If I followed your instructions properly, I picked the 3rd choice. The most likely selection only 1 green highlighted alpha-numeric code, the second choice also had one green highlighted alpha-numeric code. The third choice had 4 green highlighted alpha-numeric codes. Is that the correct interpretation of your instructions? Thank you.

    ReplyDelete
  55. HI! So, if i haven't gotten my DNA test yet, which one would you do? I want to get both sides of my family, My Mother, Father and hopefully Their mother and father (my grandparents). I currently have a large tree on ancestry. On Ancestry.com I have my mothers Sister's results, and soon my fathers Brother's Results. I have access to my Fathers Sister if necessary . I have no male to test on my Mothers side except my brothers. I've read all this info, i just don't know what I can really expect. I for sure can follow your extraction method! I'm good with computers, not genetics. Can you let me know what I will find out since when I called ancestry, they hid the fact there were no Haploid results and i had to call back a few times. Not cool. TY.

    ReplyDelete
  56. First off, thank you for all this information, it's appreciated. I'm running Promethease now but on the Morley DNA, the most likely result only had one bar of green (indicating G2-L156/PF3002). Can't find any information on that specific subclade... any incite on that or where I could find further information?

    ReplyDelete
  57. Thank you for these easy to follow guidelines. I'm just confused by the Morley results (for my husband) as they seem to all have pretty much the same amount of green in them. The suggested terminal subclades on the left columns, starting with the 'most likely' are as follows - but which is the right one?

    R1b1a2a1a2b1a2a~1
    R1b-CTS9044 (R1b-Z259, R1b-Z276)

    ----------------

    R1b1a2a1a2b1
    R1b-L2

    ----------------

    R1b1a2a1a2c1f3
    R1b-L430 (R1b-PF825)

    ----------------

    R1b1a2a1a
    R1b-L11 (R1b-L151, R1b-YSC0000082)

    ----------------

    R1b1a2a
    R1b-L150 (R1b-L23, R1b-L49)

    ---------------------

    I searched for R1b1a2a1a2b1a2a~1 online, but couldn't find anything that made any sense to me (sorry; completely new to this side of DNA).

    Thanks again for any help.
    LC

    ReplyDelete
  58. Thanks very much for this! Interestingly, after going through the steps, the "most likely" haplogroup was J1a3a. Which seems to completely go against what Ancestry gives as its ethnicity estimates - Great Britain 79%, Europe West 8%, Trace Regions 13%. Their ethnicity estimates match more closely with our known genealogy than the haplogroup seems to, but I suppose those "trace regions" could be more than trace.

    ReplyDelete
  59. For all of you running on a Mac, you have a few options. Best, but most costly would be to run something like VirtualBox with Windows installed. If this is your only, one-time need you can use the 14-day trial of Crossover. Download and instructions are here: https://www.codeweavers.com/compatibility/crossover/microsoft-net-framework-40.

    Once installed, you can run the '23andMe To Y-SNPS.exe' from within the .Net Framework 4.0 bottle and it'll work fine.

    Using the steps in the blog along with the Crossover and .Net Framework I was able to obtain my haplogroup predictions from the newer (June 2016) AncestryDNA raw data.

    Good luck.

    ReplyDelete
  60. This comment has been removed by the author.

    ReplyDelete
    Replies
    1. This comment has been removed by the author.

      Delete
  61. This comment has been removed by the author.

    ReplyDelete
  62. I am having trouble using the 23andME to Y-SNP Converter. I keep getting error message: Index was outside the bounds of the array. I've tried several times following the instructions to convert the raw data file and cannot figure out what I am doing wrong. Can someone please provide assistance? Thank you so much!
    Kathy

    ReplyDelete
    Replies
    1. same issue here :( used to work in my win 7 machine. not in win 10. now i am trying a win 7 virtual machine but 'no go' yet

      Delete
  63. I went through Promethease, searched the ISOGG database, and came up with haplogroup R! Very clear directions, thank you very much.
    I was wondering if there was a way to get more specific? Or maybe not everybody belongs to a more specific subgroup? Any help would be appreciated.

    ReplyDelete
  64. Ok so I went through Promethese but the "show" SNP option doesn't show when I click haplogroups & frequency, is that ok? Aside, from that the number at the top of the list is rs2032646(G;G), if I put that number in the ISOGG database it comes up with SNP = M90; the haplogroup E; C->G... So...this is a positive result, right? Is the haplogroup number actually supposed to be just M90? Isn't there usually a prefix number? Like I-M253 for example? Sorry, if that is a dumb question but I'm kind of lost as things aren't coming up as expected.

    ReplyDelete
  65. 1. For those on a Mac, download the free PlayOnMac software. I used it to run the script and it works perfectly.
    https://www.playonmac.com/en/


    2. 23and me says my haplogroup is “R1b1b2a1a2d3a (subgroup of R1b1b2)” but a user at FamilyTreeDNA said “23andMe uses an outdated International Society of Genetic Genealogy (ISOGG) branch structure and indeed R1b1b2a1a2d3a does not correspond to anything in their current tree”. So, I came here!

    Method one gives me this:
    Long name: R1b1a2a1a2b1a1
    Short name: R1b-Z384 (R1b-Z383, R1b-L20)

    Method two:
    Promethease gives me this: rs2032646(G;G)
    for which the ISOGG index gives this:
    SNP: M90 Haplogroup: E Y-position 21924329 Mutation C->G

    So, what is my haplogroup? E-M90 or R1b-Z384? Or something else? A bit disappointed in 23andme for providing (apparently) useless information about an important detail like this. :(

    Any help appreciated!

    ReplyDelete
  66. Still not working for me. I was able to convert to txt file but keep getting error message "no call specified for "M288 Yes i4000095 Y 2649694 T". Am I doing something wrong?

    ReplyDelete
  67. Replies
    1. I couldn't get this to work. I did 23andme. How did you get yours to format properly??

      Delete
  68. I have question though: is there a possibility that the first result may not be correct, due to the smaller number of SNPs given by AncestryDNA? (I got G2a2a, which is cool, but I just want to know if it would be better to do a Y-DNA test with 23andme just to be certain)

    ReplyDelete
  69. I'm confused. I tried both methods and got 2 different results:
    Method 1 - E-M215
    Method 2 - I-M170

    Did I do something wrong?

    ReplyDelete
  70. This comment has been removed by the author.

    ReplyDelete
  71. This comment has been removed by the author.

    ReplyDelete
  72. Hi.. I followed your instructions using the ISOGG tree and I got the BT subclade. The next longest longest green one was DE MI/YAP/m145/p205/pf1444. Is this a possibility/ does this sound right? I read somewwhere that this group is extinct. Very new at this and trying to understand. Thanks.

    ReplyDelete
  73. This comment has been removed by the author.

    ReplyDelete
  74. R1a1a1b1a3
    R1a-Z284 (R1a-Z289) My most likely haplogroup is this one. I have a question though. On wiki Isogg dna test comparison it says the SNPS tested from the Y and X. They test 1691 Y chromosone SNPs and 28, 892 X chromosone SNPS plus 440 SNPs labeled as chromosome 25 that are either from chromosome X or from the pseudoautosomal regions of the Y chromosome. Could it be that this calculator picks up the X chromosone SNPS and the pseudoautosomal SNPs and not actually the Y SNPs. Thans

    ReplyDelete
  75. so i cant use this if i tested myself (female)

    ReplyDelete
  76. MorleyDNA.com now accepts an AncestryDNA file directly. You don't have to go through the other conversion programs any more. Follow the new instructions on the site. I uploaded the zip version of my file and it ran fine.

    ReplyDelete
    Replies
    1. do they accept 23andme data as well?

      Delete