Big Y Chrome Extension

Now that the Big Y results have been coming in, recipients and administrators have begun looking for ways to work with the data. This is no trivial feat.   We’re not looking at 111 markers, we’re looking at data for over 36,000 known SNP locations, plus several hundred novel variants, each.

I have already written about what the results look like on your personal pages at Family Tree DNA. Initially, everyone is just giddy to have fully sequenced Y results, and everyone wants to know how many novel variants they have. We’re like a bunch of kids at Christmas with this year’s hot new gift. However, once the newlywed glow wears off, we begin to think about a couple of things, in particular.

First and foremost, we want to know our terminal SNP and where it falls on the haplotree.

Family Tree DNA does update the haplogroup information to include any SNP already on their tree. However, we’re all familiar with the “tree issue” at Family Tree DNA. A new collaborate tree is to be released “soon” per Bennett Greenspan, but in the mean time, we’d really like to know where our results fall on a more up to date tree.

Enter, Felix Chandrakumar, a software engineer from Australia, who has written a Chrome extension to do just that utilizing the ISOGG tree, with a few other nifty tools thrown in too, just for good measure.

First, to use this tool, you must either have Chrome, a browser by Google, installed on your PC, or install it. I flip back and forth between browsers, depending on what I’m going, so it’s not an either/or type of decision you have to make.

big y extension

When you visit this link to obtain the Big Y extension, you will be given the option of downloading Chrome, or if you have Chrome already, just installing the extension. If you have Chrome, then you’ll seen to sign on to this site with the Chrome browser to download the extension.

This extension adds several features to the Big Y results pages, including:

  • Download Big Y SNPs.
  • Download the Known SNPs Table as CSV file which can be opened in Excel.
  • Download the Novel Variants Table as CSV file which can be opened in Excel.
  • Auto-Populates SNPs into MorleyDNA Y-Tree for easy analysis.
  • Highlights Positive and Negative SNPs in ISOGG Y-Tree.

If you’re wondering how to use this Big Y extension tool, there’s a great 3 minute video on the download site as well that walks you through each step.

It’s very easy and straightforward.

First, by virtue of how extensions work, this tool adds buttons to the Family Tree DNA pages as displayed on your PC.

This first image shows the BIg Y results page without the Big Y extensions.

Big y plain

Below, the same screen with the Big Y extensions.

Big Y felix

Specifically, the new functions are shown on the toolbar as downloads for the various SNPS, by category, and in a useable format, a csv file easily converted to Excel which gives you the ability to sort and search, among other functionality.

Secondly, two options for “trees” are shown, ISOGG and the Morley tree.

Big Y felix closeup

My tree preference is the ISOGG tree, so let’s take a look.

Your derived SNPs, meaning the ones that show mutations, that have been added to the ISOGG tree are shown for your haplogroup. Red means you have tested for that haplogroup defining SNP and the result is negative, meaning you do not have that mutation, so you are referred to as “ancestral.” Green means that you do carry that mutation, so it’s referred to as “derived.”

isogg tree 1

Beginning with R-U106, which is also shown on the Family Tree DNA tree, so you can orient yourself, you can see the location of L48, the next SNP, then further down the tree SNPs Z9 and Z10 which are equivalent.

isogg tree 2

This last page shows the terminal SNP being Z326.

This of course, may not actually BE your terminal SNP. This is only the terminal SNP that has been identified and accepted as such, by ISOGG, and entered on their tree. Their tree is the most up to date, although the haplogroup names do not agree with other, earlier, trees. Before new branches can be added, the volunteers in charge of the tree structure must be able to resolve where the new SNP falls on the tree, and that has caused some massive restructuring and renaming. This is exactly why the industry is moving towards the SNP being the only identifier instead of the longer R1b1a2a1a2 type of name.

Of course, the whole point of testing the full Y chromosome is to find new SNPs. The question of when or if a personal or novel variant will be found in enough people to be considered a SNP is still being considered, but for now, the only SNPs on the tree are a subset of the SNPs already named. In other words, part of, but not all of, the 36,000 SNPs in the SNP file that Family Tree DNA compares everyone against are on the tree. Why aren’t those SNPs all on the tree yet? Plain and simple, we don’t know where those leaves fall just yet, and some labs are more open to sharing information than others – so the tree is a work in progress and will continue to be with the discovery of thousands of new SNPs via the Big Y and Full Y tests.

Meanwhile, this person had 83 high quality Novel Variants that fell someplace on the haplotree, many probably beneath Z326, but we’ll have to wait until more research is available and others have been found with these same “novel variants” to know where they fit on the tree.

I must say, I’m very impressed with Felix’s programming skills. He released this tool a mere 4 days after receiving his Big Y results. That’s nothing short of amazing!

What’s that old saying? “Necessity is the mother of invention.”

Well, thank you indeed, Felix!!! You’ve done us all quite a favor!

12 thoughts on “Big Y Chrome Extension

  1. Thank you Roberta for letting us know about Felix’s amazing BigY tool.
    If I were FTDNA, I would hire him on the spot as an IT consultant.

  2. Any chance I could still get theBig Y Chrome extension? I was out of town for the open enrollment period. Also…I need to ask 2 things..

    I use a Mac? Is your information compatible with Mac?

    I had my DNA tested with Genebase. I got a”standard maternal ancestry package” and and a “mtDNA package upgrade from HVR-1 to HVR-1 +HVR-2.”Itr provides information to genealogy bank.com

    I am completely lost in this. Do I already have the HVR-2 information you are offering?

    Do you offer a tutorial or lessons on this subject?I hoper you answer this letter….it is hard to find aa source which explains everything.

    Linda Beatie, M.D 125 Sunny Hill Dr. Petaluma, CA 94952

    • Linda, You’ve got apples and oranges and an avocado or two mixed together here. There are three kind of DNA utilized for genealogy research – mitochondrial, Y and autosomal. There were three tests for mtDNA – the HVR1, HVR2 and full sequence. There are several tests for the Y – including the Big Y test which fully sequences the Y chromosome. The Big Y Chrome extension is a tool that helps interpret the resulting Big Y data. Since you don’t have a Y chromosome, you can’t order the Big Y test and you won’t need the Big Y Chrome extension to read the results. The earlier messages this week about the mitochondrial DNA sale were for the full sequence at Family Tree DNA. The article about the mitochondrial that is incidentally on the Big Y was just an “interest” story – it doesn’t replace the full sequence. Plus, because you’re a female, it’s irrelevant to you because you can’t test your Y anyway. So you can order the full sequence mitochondrial test at Family Tree DNA or you can order their autosomal test, Family Finder, but that’s all you can order of the three major kinds of DNA tests.

  3. Roberta: Great stuff!
    Does this chrome Big Y extension look at both high and medium confidence novel variant snps
    (97 in my case) and attempt to place them on the isogg or Morley tree? Or does it look at the Big Y known snps (629 in my case) only. Big Y only looked at 25,000 of 36,000 estimated snps to arrive at 629 snps (97 novel variants) found for me.

    Also, on the R1b L21 subclades Yahoo forum, I read that FTDNA may re-run the Big Y numbers to add “low confidence” snps to the earlier Big Y runs. Mine came out on 2/27/214 .
    Have you heard of this?

    Thank you

    • Hi Steve. You might want to drop Felix a note and ask him to be sure, but I believe it looked at everything in the file. I have not heard that rumor about the low confidence SNPs, but I’m not necessarily plugged directly into that rumor mill:)

      Roberta

  4. I followed along your post and downloaded the Big-Y extension. The question I have is how long does it take to get the ISOGG SNPs to be ‘calculated?’ I’m sitting here now about 40 minutes and counting and it loaded, but at the top of the page it still says, “Please wait…” Not sure if it will come back with anything. My confidence is waning….

  5. Pingback: Haplogroups, SNPs and Family Group Confusion | DNAeXplained – Genetic Genealogy

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