Wednesday 21 August 2019

Getting the most from your new Big Y-700 results

The Big Y test changed to a completely new technology earlier this year. It now covers 50% more of the Y chromosome than previously. And so it is anticipated that the new test will discover additional SNP markers that the old technology did not detect. Furthermore, the new SNPs should be able to more accurately date the various branching points on the Tree of Mankind.

It also gives us approximately 700 STR markers whereas the previous test only gave approximately 500 STRs. As a result, the old test is called the Big Y-500 and the new one is called the Big Y-700. Going forward, all new Big Y orders will use this new technology.

For those who did the old test, it is possible to upgrade from the Big Y-500 to the Big Y-700. But for everyone who does the new test, or upgrades from the old version to the new version, it is essential that you upload a copy of your results to the Big Tree so that we can get some essential additional analyses. You will find instructions for doing so on the Big Tree website here and on the Y-DNA Data Warehouse website here but I include a briefer summary below.

What do you get from your Results?

Your results should be analysed within a week or two and you can check them by navigating to your particular portion of the Big Tree. For members of Ryan Group 2 (for example), their Terminal SNP is M756 and you will find this branch on the Big Tree here (see screenshot below). The diagram nicely illustrates their placement on the Tree of Mankind and the surnames of the people sitting on neighbouring branches to their own. This information can be very useful for determining the geographic origins of your particular direct male line and for determining if your name is associated with an Ancient Irish Clan.

Project Administrators can use programmes like the SAPP tool to generate Mutation History Trees and determine the likely branching structure of your particular "genetic family" from the time of surname origins up to the present day. This process can also help identify which Ryan's (for example) are more closely related to each other and which are more distantly related. It is also possible to date the branching points within the Mutation History Tree using SNP data as well as STR data. This process is likely to become more accurate with the advent of the new Big Y-700 data and the identification of new SNPs. It is anticipated that the new data will reduce the number of "years per SNP" from about 130 to about 80 years per SNP. You can read more about this here.

You can also click on your surname above your kit number for an analysis of your Unique / Private SNPs. These may prove useful in the future for defining new downstream branches in the Mutation History Tree and for dating new branching points. But this very much depends on new people joining the project and undertaking Big Y-700 testing (so that we can compare apples with apples). And as this is a new test, it is likely that we will have to wait some time before we begin to see real benefits from it.

Creating a Link to your Big Y results

In order to create a downloadable link to your Big Y results, first log in to your FTDNA account and go to your Big Y Results page ...

Then click on the blue Download Raw Data button ...

Then you need to create a link to two separate files - your VCF file and your BAM file. The VCF file is used for placing you on The Big Tree. The BAM file is used for high-end technical analysis by the folks at the Y-DNA Data Warehouse. You can see some of the results so far on their Coverage Page here (and if you like you can search for kits by surname, including your own).

1) to create a link to your VCF file, right click on the green Download VCF button, and then click on "Copy link" from the drop-down menu. You will later paste this link into the the "Download URL" box on the Submission Form.
Alternatively you can simply (left) click on the green Download VCF button and this downloads a 10 MB file to your computer. This can then be directly uploaded via the Submission Form below. However it is preferable (and less problematic) to generate a link instead.
2) to create a link to your BAM file, click on the green Generate BAM button. You will then get a message that "Your Big Y BAM file is currently being generated" (see below). This generates a very large BAM file ... but it takes several days to prepare so you will have to come back to this page in a few days time! Put a reminder in your diary / calendar!

Uploading your VCF file

Having created the first link (to your VCF file) and copied it, click here to go to the Y-DNA Data Warehouse and fill in the form with your standard information - email, kit number, surname of your paternal MDKA (Most Distant Known Ancestor), and (most importantly) the link to your file - you do this by pasting the link you copied earlier into the "Download URL" box underneath the heading "Raw Data Upload" at the bottom of the page.

If you want to upload the actual file itself (rather than a link), click on the blue Direct tab under "Raw Data Upload" and then click on the "Choose File" button and attach the file from where you downloaded it onto your computer (on my laptop, the "Choose File" button appears to be slightly hidden under some text but it works if you click on the start of the text). 

Don't forget to tick the checkbox to confirm you agree with the Data Policy and then click the blue Submit button.

Uploading your BAM file

Several days later, come back to this same place to get a link to your newly generated BAM file. So, navigate to your Big Y Results page, and after clicking on the blue Download Raw Data button, you will find that the BAM file has been generated. DO NOT DOWNLOAD IT - you don't need to and it is way too big. Instead, click on the green Share BAM button and then the green Copy button in order to copy a link to your BAM file. You will share this link in the next step.

Then go to the Y-DNA Data Warehouse and fill in the same form as before BUT ...

  1. select Other for the Testing Lab
  2. enter your Kit ID Number 
  3. leave everything else on its default setting
  4. paste the link to the BAM file in the "Download URL" box underneath the heading "Raw Data Upload"
  5. tick the checkbox to confirm you agree with the Data Policy and then click the blue Submit button

Maurice Gleeson
Aug 2019


  1. This is a wonderful article. I intend to share it with members of my project in hopes that they understand why I want them to do Big Y testing.

  2. If my experience is any indication, you'll need to give them some time to add your Big Y results. Don't expect to see immediate results in the Big Tree.

  3. Great article. Thank you. Here’s my question. My brother took the Y test 12 years ago. I upgraded to 67 markers several years ago. Yet, in all that time, not only do we have very few matches, but NONE have our surname and none are close enough in time to figure out. I understand this may mean an adoption or something along the way and our surname may not be linked to a Gould line.
    I don’t know what the Big Y test would reveal to us that would make it worthwhile. I’ve met with professional genetic genealogists and the FtDNA reps at conferences. All they tell me, as they shake their heads, is "you have a very tough case."
    I’d like to solve this mystery before I’m gone. I’m a senior citizen and a very experienced genealogist.
    How would the Big Y test benefit us?

    1. Excellent question, Diane. It can be a lonely place sitting all alone on an isolated branch of the Tree of Mankind! FTDNA are right when they say it is a very tough case! It suggests that you sit on a very isolated branch of the Tree of Mankind. At this stage we don't know whether you simply have a surname with a rare DNA signature or whether there has been some switch along the way (adoption, etc). However, there are a few things you can do:
      1) upgrade to 67 markers - you have already done this. Some times matches that are "hidden" at the 37 marker level can be revealed at the 67 marker level. E.g. a person with a GD of 5/37 to you will not show up as a match at the 37 marker level because he falls above the threshold of 4/37 for declaring a match. But if he tests a further 30 markers and upgrades to the 67 marker level, then if he has no additional mutations in the additional 30 markers, his GD will now be 5/67 which IS declared as a match.
      2) upgrade to 111 markers - similarly to above, hidden matches may be revealed at the higher level of testing. However the closest GD will be 8/111 and this is not particularly close. It may reveal a few Gould's though.
      3) Join all the relevant Haplogroup or Geographic projects (for free), see in which group you are placed (this may offer clues), and if no clear way forward is obvious, email the Admins and ask them for advice.
      4) Big Y test - this will place you firmly on the Tree of Mankind and will show you either to be on a very isolated branch with no close neighbours (i.e. no common ancestor for >2000 years), or it may identify surnames to which you are related in the past 1500 years or so. It is unlikely to identify any neighbours with whom you share a common ancestor within the last 500 years or so - they would have already turned up in your STR matches if they were there. So the test is of limited value in helping to find close matches but it can still give you some clues to your origins some 1000-2000 years ago.