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**Armando** · 8 February 2016, 11:23 AM

First you should tell us if you want Y-DNA matching or not, how much resolution you want for the Y-DNA SNPs (if any), and if you care to have an mtDNA haplogroup.

Once you do a transfer to FTDNA you get three CSV files. One for Y-DNA with all of the 13, 600+ SNPs tested and their alleles, an mtDNA CSV file with some of the SNPs tested, and a Y-DNA CSV file with just the positive SNPs. The two Y-DNA SNP files confuse people because they have the exact same name but are located in two different places and have different results. The FTDNA haplotree only shows the positive results from Geno 2.0 and sometimes places people in the wrong subclade because they don’t have the negative SNPs and the Geno 2.0 NextGen test has a lot more false positives than there should be. You don’t get any STR results either so no Y-DNA matching. Geno 2.0 only tests SNP markers. If you want the autosomal file you have to pay $39 for Family Finder then you get the results, the file, and matching. You don’t get mtDNA matching and would have to buy a $199 mtDNA Full Sequence (FMS) test to get all of the mutations as well as matching.

So with Geno 2.0 for $149.95 (sale price) +$39 which is $188.95 you get 13,600+ Y-DNA SNPs (which could have contradictory placement due to too many false positives and you still might not get the terminal SNP an SNP pack could provide), no Y-DNA matching, autosomal DNA with a file, matching, and ethnicity estimates, and an mtDNA haplogroup without matching. If you tack on a Y-STR 37 that’s an additional $149 for a total of $337.95. If you wait for a sale on the Y-STR 37 you might save $10 or $20 more.

At FTDNA the FF and Y-STR 37 kit would cost $99+$149+$12.95 (shipping) which is $260.95 and provides Y37 matching, a predicted major haplogroup such as R-M269, no Y-DNA SNPs, autosomal DNA with a file, matching, and ethnicity estimates and of course no mtDNA haplogroup. If you add on a $99-$119 SNP pack then the total is $359.95 -$379.95 which is $22-$42 more but that is easily justified by the proper placement and SNPs that are more relevant to your haplogroup being tested. The caveat being that Geno 2.0 NextGen can many times provide a person with an SNP that is much more recent than an SNP pack. It’s a roll of the dice in that regard.

**JanN** · 8 February 2016, 09:34 PM

2 YSNP files from Geno 2 next gen and FTDNA uses the one without the negs?

Thanks for your helpful reply. I was confused about the comments I had read here on the transfers generating "false" SNP tree placements. Why can't we use the other YSNP files (that contains the negatives as well) to create the FTDNA "tree branch or leaf" placement ?

Is there any way you can get the raw data from Geno2 without a FTDNA transfer and upload somewhere else to get access to more of your SNP's tests (assuming the Geno2 next gen tests, as it states, over 750K markers?)..like a BAM file ? If I could do that then I could just buy a YSTR37 for matching purposes and be more certain of my YSNP placement, have a lot more data. I'd also buy the FF conversion if it gave the same as buying one at FTDNA.

STR's seem to me to be repeating sequences of SNPs at given points on a Y chromosone, it seems to me that one really does need the SNP to be certain of your YDNA? ie the STR could have occured after a differing SNP value..and you wouldn't actually be related at all?.or is that not a problem

I was considering a YElite 2.0 ..which gave a fairly accurate read length of 250 , all the SNP's over 400 STRs ..so no more tests needed and had a special around Xmas of about 650.. but now they have reduced it to a Y Elite 2.1 which only has a read length of 150bp and somewhere over 30X ..so may not be as accurate and has increased in price. It is a little pricey and a bit of an overkill for me though.
I also love the projects and matching on FTDNA..although the YElite provide free mtDNA like BigY used to do... (where it comes out OK..which it may not do with a shorter read length and fewer repeats)..and ALL the STRs, correctly positioned.
I've read many posts where BigY testers who still had to pay for additional SNP packs as theirs SNPs were not covered in the BigY . You also have to buy STR's separately so you have no idea where they occur on your YDNA, and it works out more ..if you want to go that far!
Basically I only have one lot of money to spend.. which I'm been saving for many years..so I can't just keep testing but my Dad has dementia so I can't wait much longer either.

Also with the Geno2 next gen..if I purchase the FF transfer do I get everything ie as many SNPs as if I had purchased thru FTDNA or are some SNP's not covered?

**The_Contemplator** · 9 February 2016, 12:14 AM

The Geno 2.0 Next Gen test and its previous incarnations seem better suited for the people who want just general information about their ancestry while making the most out of their dollars. However, it sounds like you want the most information you can get but you are looking to not be wasteful with your money. If so, then maybe the Geno test is not the best fit for you.

I think the reason the Y Elite test covers the amount it does is to attract consumers that want the complete test. It has no matching system that I am aware of unlike FTDNA's tests. FTDNA tries to cover what will be most useful to have some sort of balance between cost and benefit. I don't know if Y Elite is good, but there does not seem to be a lot of interest for that test compared to Big Y. So who knows?

None of the SNP tests or packs will find new SNPs unique to you and closest relatives. Only a test like Big Y can do that. Big Y is at $575 right now. You could wait for a sale, but I don't imagine there will be one any time soon. The Big Y does not become an option until you order a Y-STR marker test (37, 67, 111), but I have heard you can ask to order it and bypass the Y-DNA STR test.

You can upload the BAM file to YFull for analysis ($49). They will give you a haplogroup assignment that may differ from FTDNA since it will use your data to build new SNP branches if you happen to share that with at least another person. Otherwise you have some private SNPs that could form future branches after someone else with them uploads their BAM file. Just take a look at the YFull tree. It gets an update every few weeks.

YFull will also show you the STR data from the BAM file. Looking at mine, I see I have 496 STRs listed. Out of those, 415 are considered reliable. From the rest, 12 are uncertain which means they have some data but can't be too sure and 69 are N/A (no calls). Before the Big Y I had taken a Y67 STR test. I compared the results with the Big Y STRs I have. Comparing those 67 from Big Y data, 54 were reliable and are exactly the same to what FTDNA had for me. The rest had no calls from the Big Y but I have data for on the Y67.

Keep in mind that FTDNA does not do cross-test matching. So if a potential match took a Y-111 test but you took a Big Y and you both are suppose to be matches, you won't see each other. The Y-STR marker database is separate from the Big Y matching database. YFull has its own SNP and STR matching systems for people who have submitted their BAM files.

Out of the 3 types of tests, mtDNA is said to be the least useful. If you do want it, you will want the Full Sequence as the rest will be too vague to narrow down which are the distant relations not worth perusing and which are worth chasing.

Seeing as you feel time is not on your side to test your father, you could just order a blank kit in the mean time. At the top of this page click on Customer Support. Then Open a request in the Support section to use the contact form. Tell them you wish to order a blank kit (or more than one if you think you might test others later). Ask for extra swabs/vials so that instead of getting 2 swabs/vials you get 4. This does not cost extra. The blank kit is just that, a collection kit with no test tied to it. It will cost $12.95 per kit within the US. It is the same price it would have cost in addition to any test you might have ordered so there is no down side.

This way at least you get some piece of mind that you collected a sample from your father while you decide what tests to order. After confirming your blank kit order, you will get an email with the kit number and password. In the order history you will find a PAY NOW link. You can pay for the kit there or wait until you order a test.

**dna** · 9 February 2016, 01:48 AM

The following is only my personal opinion

@JanN, if knowledge is your priority:

Family Finder (could be the last test),
full mtDNA,
Y-DNA37 (or Y-DNA25 or Y-DNA12, if the $$$ difference is critical),
the relevant SNP pack.

Matching is more than genealogy.

Mr W

P.S.
You can always disable matching at FTDNA.

**JanN** · 9 February 2016, 06:08 AM

Reply To Contemplator and all

Thanks for your detailed help.
I think I agree re the Geno2 test. I thought with the 750K SNP's covered it may be more detailed, but I can see no way of finding out if and what raw data you can get..although I've learnt a lot more today.

Here's my concern re the Big Y. If it had been earlier I would have tested for it , got the BAM , uploaded it and got the STR's & likely also have done the FF (atDNA) with FTDNA for my father. (especially before they deleted the medical SNP's)
I would have had everything..the atDna, the mtDNA, and the YSNP's and STR's in enough detail for a accurate placement on the tree (I may have had to order more individual SNps , but not many) I needed for a cost I could afford (especially when the BigY had $100 vouchers off earlier). This is likely when you tested at FTDNA?

As the Big Y stands now..
the Big Y at FTDNA some time last year deleted all mtDNA ..forcing you to pay extra sadly as the coverage should have been good enough at 50X. (Also the Big Y do not include many of the needed SNPs for terminal leaf placement on the trees. They are available in the add on packs (according to posts I've read)..This doesn't happen to everyone though.

Now according to the FTDNA do NOT cover STR at all?

Security check

https://www.familytreedna.com/learn/y-dna-testing/haplogroups-snps/order-str-before-snp/

"Do I have to order a Y-chromosome DNA (Y-DNA) STR test before I take a SNP test? Yes. If you do not have a Y-DNA STR test, you will not be able to view your haplotree information."
I find this to be confusing as I thought the SNP's should determine your haplogroup?

Security check

https://www.familytreedna.com/learn/y-dna-testing/big-y/

"55X to 80X average coverage. Around 11.5 to 12.5 million base-pairs of reliably mapped positions of non-recombining Y chromosome." from technical on above url, no read length specified, but coverage is excellent and what I'd like!

"Will you report Y-STR results from Big Y testing? No, we will not.' last question on page.

Does anyone who has tested since September know if the STRs are in the BAM file or deleted as well? I was originally saving to get the Big Y until they stated they do not cover the STRs and now the mtDNA data is not there and
the BAM files are no longer available. (hopefully a future remedied storage issue, but I pause for thought after having the mtDNA removed).
Really I'd have preferred to pay a little more and get the mtDNA coverage in the BigY. I did read posts where people were requesting reruns as the mtDNA wasn't "full or clear" enough..not enough reads and that wasn't fair on FTDNA as it was only in there but not "guaranteed or paid for".

So now a BigY may not provide all the SNP's you need to be placed in the tree..doesn't give STR's (and no BAM if they are still included in it), doesn't give a haplogroup without the Str's previously ordered? (above), and doesn't give you the additional mtDNA which you have to add on.

At Full Genomes , The Y Elite 2.0 was 250 base pair read length and 50X coverage. Not only here but in several forums folk were stating it was acurate and also provided a reasonaly good if not full mtDNA (this was not guaranteed )., and all the SNPs. https://dnatestingchoice.com/ancestr...-genomes/640bp
Unfortunately they have dropped the read length this month to 150 and coverage to 20X with YElite 2.1...so it's unlikley when these come back that the accuracy will be as good and the mtDNA will not be covered enough (unless lucky). Price up as $100 off no longer available at present too.

so it seems DNA testing is not as good as it was last year...

Hence my wondering what the Geno2 test provided in more detail, but I agree with you, It appears to be aimed at people who want just general information about their ancestry not at those who want the raw data and detail.

I know I can currently get the YSTR 37 for a discounted price of $119 if I go thru a group and use the RT discount..but that would replicated in the the BigY or YElite, so be mostly a waste of money provided I can get a BAM file including STRs.

I did email Geno2 last year and received a friendly reply answering in part but they didn't know about the BAM file etc but escalated the query up into outer space...so I assume the answer is no .. at least not for a customer? The FTDNA info says you can..but not how much of it.

I'll do the rest of my reply on the atDNA and mtDNA in another post as this is too long...

**JanN** · 9 February 2016, 06:29 AM

reply part 2 on atDNA and mtDNA

I have ordered the mtDNA FS for my Mum (actually for myself as its theoretically the same) earlier today and the Family Finder (atDNA) for MUm (just about to post back), both at FTDNA. I am really interested in my Mum's mt line of ancestry but paper records have been lost in Nth Ireland. Word of mouth suggests a Scots Irish clan and some earlier French somewhere on that side, ..hence the mtDNA. I realise it will likely not be much use but its my only chance for the future.

( I am really disappointed that it looks like I'm testing the atDNA (Family finder) a year or two too late... as all companies (ancestry, FTDNA and Geno2 next gen) state they have removed any known medical related SNPs or reduced at 23&me, so you miss out on on health related SNPs ie unless you go for the full genome at Full genomes for $895(only 15X, so likely not accurate enough). To get comparable accuracy to the BigY , the Full Genomes it would be $1600 as at Jan16 and the raw data fills a full removable HDD!
While I would never have liked any medical info reported on, I would have liked to be able to analyse myself or via a different site via a raw data file in some format . I've also noticed "medical" conditions run thru our families. It's one of the reasons I have been doing ancestry research for the past 30 years or so. That suggests to me that the medical SNPs must be a significant part of the identifiable changeable SNPs that help uniquely identify you and your family, so their deletion , I suspect,? makes the family finder not as robust ie not able to go back as many generations or match as many people who are related and would reduce segment length of the matches as well I would think? There has been no such suggestions though.(perhaps as more SNPs were added at the same time as these significant SNPs were deleted?)

I'd definitely be getting many more FF tests for if the Medical related SNPs had not been removed, and would definitely get one for at least my father, myself and my brother!..run thru Promethease I've heard a year or so ago..but that will not show anything now I assume.

I 've looked at ancestry and 23&me as well but found FTDNA looks to be the best of those three for many reasons so I'm disappointed inthe cutting back on the mtDNA, BAMs (perhaps the STRs in them?), and the medical data...
I had thought the DNA testing could only get better and cheaper.
I'm still considering just getting the atDNA (Family Finder)for my Dad too at FTDNA, and leaving the Y (and mtDNA)for later,perhaps via my brother and cousin if I can get them to test as Dad will be past it later.
Thanks everyone.
Hope the BigY BAM files do come back just as they used to be., maybe one day someone will tell us how many SNPs approx are in the raw data files you can get from Geno2. I read that you can only get them after you transfer to FTDNA..but I could be wrong.

**Armando** · 9 February 2016, 07:48 AM

Originally posted by JanN View Post

Thanks for your helpful reply. I was confused about the comments I had read here on the transfers generating "false" SNP tree placements. Why can't we use the other YSNP files (that contains the negatives as well) to create the FTDNA "tree branch or leaf" placement ?

Is there any way you can get the raw data from Geno2 without a FTDNA transfer and upload somewhere else to get access to more of your SNP's tests (assuming the Geno2 next gen tests, as it states, over 750K markers?)..like a BAM file ? If I could do that then I could just buy a YSTR37 for matching purposes and be more certain of my YSNP placement, have a lot more data. I'd also buy the FF conversion if it gave the same as buying one at FTDNA.

STR's seem to me to be repeating sequences of SNPs at given points on a Y chromosone, it seems to me that one really does need the SNP to be certain of your YDNA? ie the STR could have occured after a differing SNP value..and you wouldn't actually be related at all?.or is that not a problem

I was considering a YElite 2.0 ..which gave a fairly accurate read length of 250 , all the SNP's over 400 STRs ..so no more tests needed and had a special around Xmas of about 650.. but now they have reduced it to a Y Elite 2.1 which only has a read length of 150bp and somewhere over 30X ..so may not be as accurate and has increased in price. It is a little pricey and a bit of an overkill for me though.
I also love the projects and matching on FTDNA..although the YElite provide free mtDNA like BigY used to do... (where it comes out OK..which it may not do with a shorter read length and fewer repeats)..and ALL the STRs, correctly positioned.
I've read many posts where BigY testers who still had to pay for additional SNP packs as theirs SNPs were not covered in the BigY . You also have to buy STR's separately so you have no idea where they occur on your YDNA, and it works out more ..if you want to go that far!
Basically I only have one lot of money to spend.. which I'm been saving for many years..so I can't just keep testing but my Dad has dementia so I can't wait much longer either.

Also with the Geno2 next gen..if I purchase the FF transfer do I get everything ie as many SNPs as if I had purchased thru FTDNA or are some SNP's not covered?

The false SNP tree placements are probably due to the technology used to test the SNPs. It’s chip based vs. true Next Gen sequencing. You can use the CSV file to cross reference the alleles with other databases such as ISOGG SNP tree, Ray Banks sites, the BigTree by Alex Wiliamson, Ybrowse by Thomas Krahn, or anything provided by a haplogroup admin. But you have to do the work or you have to give the file to someone that is willing to do the work for you. Since a lot of important SNPs aren't tested by Geno 2.0 NextGen it sometimes makes it harder to interpret the results.

There are only about 13,600 Y-DNA SNPs tested by Geno2 and the only way to get those is with the transfer. The 750,000 SNPs that you are quoting are mostly due to the 700,000 or so autosomal SNPs. BAM files are for very large files due to much higher sequencing. Yes, you could by a Y-STR37 for matching purposes which is what I had pointed out. My understanding is that the FF conversion is the same as buying one at FTDNA.

STRs testing results are tied to specific STRs. STRs are normally better for more recent genealogy. SNPs are better for more ancient ancestry depending on how well your sublcade has been tested. If you don’t match in SNPs that are estimated to have occurred beyond a genealogical time frame with other people that have had the same level of reliable testing then you don’t have an ancestor in common with those people in a genealogical time frame. If you are lucky enough to have tested down to an SNP that is from a genealogical time frame and you do match another person then you have an ancestor in common within that time frame. SNPs are more reliable than STRs provided that you have had the right type of testing.

If you can afford YElite then you should get it and not waste anymore time discussing Y-DNA SNP testing. If you want Y-STR matching at FTDNA you will still have to purchase a Y-STR test at FTDNA and the same goes for mtDNA. If you can afford Y-STR testing plus BigY then that would be better except for lower SNP resolution and maybe needing a YFull analysis.

You shouldn’t have to purchase additional SNP packs after purchasing a BigY test. You might need a single SNP test such as DF27 but that is very unusual since so many downstream SNPs have been identified. YFull can extract your STRs from the BigY test but you still won’t have matching with the FTDNA database. They aren’t as reliable as the STR tests from FTDNA though.

Yes, you get as many autosomal SNPs with the FF transfer from Geno 2.0 NextGen as if you had purchased through FTDNA.

**Armando** · 9 February 2016, 08:03 AM

Originally posted by JanN View Post

maybe one day someone will tell us how many SNPs approx are in the raw data files you can get from Geno2. I read that you can only get them after you transfer to FTDNA..but I could be wrong.

There are about 13,600 Y-DNA SNPs in the data file from Geno2 and the file can only be acquired after transferring to FTDNA. It is in CSV format. Geno 2.0 NextGen isn't really NextGen testing.

There are many very important Y-DNA SNPs missing from the Geno 2.0 NextGen test which is a big problem apart from the large amount of false positives.

**The_Contemplator** · 10 February 2016, 12:27 AM

Well the BAM file will come back once they sort out whatever issues they have with their system. Based on FTDNA's estimate it should be back by the time you get Big Y results if you decide to order one this month or later. They didn't take out the STRs. They simply don't use them (report them) as they don't consider them as reliable as their STR marker tests. I ordered my Big Y October 2015 and got the results November.

I'm not completely sure why they took the mtDNA data out, perhaps because it was incomplete. It is my understanding that the Y chromosome has a portion that is similar to the X chromosome. Maybe that is how the Big Y test got some of that mtDNA information. FTDNA may have seen that as unreliable or maybe so it doesn't hurt their mtDNA sales. Maybe even both?

As for why some people might still need some SNP tests after Big Y, I think it has to do with the nature of the Big Y test. Big Y is more of a let's break this Y up and see what we find than let's look if these specific SNPs are in the Y.

Yes, I tested when there was a $100 off coupon. They seem to give these out some time after you get your STR results. Or at least that is when I got mine. I got another kit I'm waiting on STR results, I'll see if they mention the Big Y after those results. Though there was more of a discount during the holiday sale this past November and December. It sounds like FTDNA is gearing up for some changes to Big Y. It could be that they will add some new functionality or tweak something. They may even drop the price a bit more. Wasn't the original price like $675? Something like that, so it could still come down. You could also just wait for the next big sale if you are patient enough.

Promethease should still work with your FTDNA FF (atDNA) data. Unless I missed something, I don't know what medical SNP's you could be referring to exactly. I know FTDNA has some message about trying to avoid some medical stuff but I don't think that means they stripped it clean. Maybe that was more towards 23andme which had to take some out from their test. However, remember that it is one thing to not report some medical SNP data and another to not include it in the raw file. Promethease is just $5, so you could still give it a shot.

One more thing, if you are interested in the atDNA databases, you could consider getting a test done at Ancestry and then transferring the data to FTDNA for more bang for your buck. The transfer would only cost $39 or if you can get 4 other transfers to take place it would be free. Either way, transferring to Gedmatch is a plus and free.

As for Big Y coverage and read length, I know that YFull gives some stats for that. So if it is of any help, based on my kit this is what YFull tells me.

ChrY BAM file size: 0.47 Gb
Reads (all): 7545183
Mapped reads: 7545183 (100.00%)
Unmapped reads: 0
Length coverage: 14337591 bp (55.89%)
Min depth coverage: 1X
Max depth coverage: 7734X
Mean depth coverage: 60.08X
Median depth coverage: 41X
Length coverage for age: 7945582 bp
No call: 11315975 bp

"Reads" - aka "DNA fragments"

**KATM** · 10 February 2016, 07:12 AM

Originally posted by Armando View Post

There are about 13,600 Y-DNA SNPs in the data file from Geno2 and the file can only be acquired after transferring to FTDNA. It is in CSV format. Geno 2.0 NextGen isn't really NextGen testing.

There are many very important Y-DNA SNPs missing from the Geno 2.0 NextGen test which is a big problem apart from the large amount of false positives.

Armando, I have a so-far unused Geno 2.0 NextGen kit, intended for a male who will likely be in the "I" haplogroup (he is of Scandinavian ancestry on his direct male line), although you never can tell. Are the missing SNPs all in the R1b area, or do you know of any place I can go to read further about which are the important Y-DNA SNPs that are missing from this test? I am checking the threads at Anthrogenica.com in the meantime.

**Armando** · 10 February 2016, 11:09 AM

Originally posted by KATM View Post

Armando, I have a so-far unused Geno 2.0 NextGen kit, intended for a male who will likely be in the "I" haplogroup (he is of Scandinavian ancestry on his direct male line), although you never can tell. Are the missing SNPs all in the R1b area, or do you know of any place I can go to read further about which are the important Y-DNA SNPs that are missing from this test? I am checking the threads at Anthrogenica.com in the meantime.

It's hard to determine all of the important Y-DNA SNPs that are missing or which haplogroup is affected the most. I can only say that it is enough that it can't prevent ambiguous or contradictory results 100% of the time.

I am still in the process of building a database of reference SNPs. I only have the ISOGG SNP reference so far. Out of the 13,600 Geno 2.0 SNPs there are 3,520 that match the SNPs in the ISOGG database. 688 are Hg R. 262 Hg I. Compare that to what ISOGG has which is about 2,346 Hg R SNPs and 1039 Hg I SNPs. So R does have a lot more missing than I. That probably would change if I were to have an updated reference database though.

**KATM** · 10 February 2016, 02:01 PM

Thanks, Armando. I would hope that the Geno 2.0 Next Gen test would at least be accurate enough for hg I to determine I1 vs I2. It will all be moot for me, anyway, since the intended testee is not too eager to use the kit, so far.

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Geno 2.0 Next Gen - what detail ? and comparison to FF and mtDNA & Y-DNA

Geno 2.0 Next Gen - what detail ? and comparison to FF and mtDNA & Y-DNA

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