Uploading your New Big Y 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. There are several people within the project who have done this upgrade and we will look at these results in a subsequent post.

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.


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

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 the particular portion of the Big Tree. Here you will see your placement on the Tree of Mankind and the surnames of the people sitting on neighbouring branches to your 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. Gleeson Lineage II members are surrounded by O'Carroll's (from nearby Offaly), McMahon's (from neighbouring Clare), McCarthy's (from North Cork), and Treacy's (from Galway). You can see these neighbouring branches in this portion of the Big Tree here.

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 Gleeson's are more closely related to you 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.

Maurice Gleeson

Aug 2019