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View Full Version : FTDNA haplotree problems and using Big Y SNPs in their haplotree?



TigerMW
03-10-2015, 11:36 AM
Dennis Wright, a project admin, started this thread in the L21 forum on March 9th but this is pretty generic so I'll restart it here. There are clearly problems caused by FTDNA's haplotree system being behind, people using it for test advice and not going to forums, etc., etc.


Its is great that FTDNA are now showing some SNPs below the old favourites of M222, L1066, L1308, L226 etc, on the Haplogroup Tree, but when are FTDNA going to include the results from our Big-Y testing on the tree for each person who has taken that test?

I am still shown as L226 confirmed, and while I have Sanger tested FGC5628 and shown negative, (correct) the tree still invites me to test FGC5660, DC8 and FGC12290.

I have tested Big-Y and my results were one of the first batch released, 25505 Wright, with my VCF file dated 26 Feb 2014 and my BAM file dated 03 April 2014. FGC12290 is my terminal SNP, as I, along with 69433 McGraw am derived for it. As this is our terminal SNP, it constitutes a branch in the L226 tree, and it has been chosen by FTDNA as a suitable SNP to offer others.

Why am I not shown positive for this SNP?

As the administrator of the R-L226 project, I am having to alert those that have already tested Big-Y, that there is no advantage in individually testing these SNPs under L226 as they have already been tested every one of them with their Big-Y test.

As a co-admin for the Z253 project I have seen several Z253 men that have already tested Big-Y, but are now ordering the Z253 plate test!
They have already tested every SNP on that plate in their Big-Y.

The plate tests and individual SNPs are designed to help those who HAVE NOT tested Big-Y.

Are other admins having the same trouble?
When will FTDNA start posting Big-Y SNP results onto each individual's Haplogroup Tree?
--
Dennis Wright
Donnchadh Mac an tSaoir
Irish Type III R-L226
"We are merely the present-day custodians of our Ancestors genes."

TigerMW
03-10-2015, 11:47 AM
Dennis Write wrote,
"As the administrator of the R-L226 project, I am having to alert those that have already tested Big-Y, that there is no advantage in individually testing these SNPs under L226 as they have already been tested every one of them with their Big-Y test."

I generally agree with the main them of this point, that administrators, to be diligent, are forced into extra to educate about the individually testing SNPs when one already has done a Big Y or some other test.

However, specifically, there can be good reasons, from questionable coverage, Sanger Sequencing verification, etc. so it is not a carte blanche answer. A discussion is needed.

Dennis wrote,
"As a co-admin for the Z253 project I have seen several Z253 men that have already tested Big-Y, but are now ordering the Z253 plate test!
They have already tested every SNP on that plate in their Big-Y."

I agree this can appear non-sensical but there are cases where people literally want to run tests that are redundant for reasons of validation, "piloting", etc. For some individuals, the amounts of money is not of consequence, literally, so I never challenge individual members underlying motivations and if they want to show up in every system twelve ways to Sunday that's okay. It's an individual choice.

The problem is those who are ordering without realizing that may not need too. This is where the extra work is forced on the project administrator, if they are trying to be diligent. I don't do this in large projects, but in my L513 project I have the order admin notification email turned on so I see new orders. If one doesn't make sense I email the individual. Many times they change their mind as a result of the conversation and so far FTDNA has been changing the order or generally complying with the individual members' requests.

In the case of the Z253 pack, I wonder if the project admins sent out a broadcast email to describe the offering and its applicability? I think FTDNA builds these packs in conjunction with the project admins so it would make sense to time a broadcast email to the project. I don't have a fixed SNP pack for my subclade so I don't know if there are problems with this, but seems like a reasonable way to proceed.

TigerMW
03-10-2015, 12:12 PM
Dennis wrote,
"I have tested Big-Y and my results ... Why am I not shown positive for this SNP?"

This is rhetorical but I will express the overt problem or complaint and it is legitimate. FTDNA Big Y SNPs do not should up on the Y DNA SNP results web page for a project unless they have passed through the filtering system for FTDNA's haplotree. I don't really know how it works but they attempt to display relevant derived SNPs and ancestral downstream SNPs.

Does anyone know how this works? I think the idea is appropriate, but I suspect the root cause of the problem is FTDNA just doesn't have the haplotree and their filtering process correct. I'm not sure. Any feedback or investigations on this?

I don't really use the FTDNA forums but I wonder if we should post about this over there and see what they say?

Joe B
03-10-2015, 03:16 PM
Dennis wrote,
"I have tested Big-Y and my results ... Why am I not shown positive for this SNP?"

This is rhetorical but I will express the overt problem or complaint and it is legitimate. FTDNA Big Y SNPs do not should up on the Y DNA SNP results web page for a project unless they have passed through the filtering system for FTDNA's haplotree. I don't really know how it works but they attempt to display relevant derived SNPs and ancestral downstream SNPs.

Does anyone know how this works? I think the idea is appropriate, but I suspect the root cause of the problem is FTDNA just doesn't have the haplotree and their filtering process correct. I'm not sure. Any feedback or investigations on this?

I don't really use the FTDNA forums but I wonder if we should post about this over there and see what they say?
It's about time the haplogroup administrators made a concerted effort to strongly encourage the correction of the FTDNA haplotree. Their tree is bad and it's just not right that people are ordering phylogenetically worthless SNPs. What happened their promise of working with haplogroup projects to correct the FTDNA tree?

Petr
03-10-2015, 03:33 PM
One example of strange behavior. Based on Y37 results and placement in the project to:
6. ..>Z280>CTS1211>Y35>CTS3402>YP237>YP951>YP977>YP1018-x (YP1018, YP1017 and/or Big Y needed)
I ordered CTS3402 test and indeed the result was positive. But the predicted haplogroup is still R-M512:

http://i59.tinypic.com/11aijjr.png

and in the project group, the field is in red color R-M512.

I know that it was not necessary to test for CTS3402 but I wanted to have green confirmed haplogroup CTS3402 visible...

Cofgene
03-10-2015, 04:07 PM
It's about time the haplogroup administrators made a concerted effort to strongly encourage the correction of the FTDNA haplotree. Their tree is bad and it's just not right that people are ordering phylogenetically worthless SNPs. What happened their promise of working with haplogroup projects to correct the FTDNA tree?


My understanding is that FTDNA's hands have been tied due to a contractual agreement with utilizing the Geno 2 result tree. Sometime this year we could see a change. But the underlying problem of improper identification of novel SNPs needs to be addressed within their database before they move forward with revising their haplotree. There are probably >35000 SNPs identified that FTDNA is not compariing Big-Y results against. The haplogroup projects know what SNPs and INDELs are relevant for a new tree but until FTDNA updates their internal database references we are not going to see changes.

Put a blurb on your project to ALWAYS contact a relevant haplogroup project before ordering SNPs.

vettor
03-10-2015, 05:37 PM
My understanding is that FTDNA's hands have been tied due to a contractual agreement with utilizing the Geno 2 result tree. Sometime this year we could see a change. But the underlying problem of improper identification of novel SNPs needs to be addressed within their database before they move forward with revising their haplotree. There are probably >35000 SNPs identified that FTDNA is not compariing Big-Y results against. The haplogroup projects know what SNPs and INDELs are relevant for a new tree but until FTDNA updates their internal database references we are not going to see changes.

Put a blurb on your project to ALWAYS contact a relevant haplogroup project before ordering SNPs.

not true about ftdna tied with Nat geno, because Natgeno is the only one that so far use the FEB.2014 mtdna tree ( latest ), and the only one that accurately predict my ydna.

So, Natgeno is correct for me for both ..........while Ftdna in regards to mtdna is completley off................strange how their ( ftdna ) project people are correct and different from ftdna main group in regards to mtdna.

The most disturbing issue is the FAILURE of ftdna to accept all the NEGATIVE snp found in Natgeno2 tests and the prevention of moving them when you transfer your results........very very distubing problem