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BIG Y and SNP Discovery This area is for talk about BIG Y results.

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  #11  
Old 9th March 2018, 11:19 PM
dna dna is offline
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W. (me) has a 4th cousin (C.).

Big Y results for C. are missing the final SNP that W., W. grandfather brother, and other men (unrelated to W. or C.) have.

Once that SNP (of BY variety) becomes available for purchase, we will of course order it. However, the discussion impressed on me that a positive result would not be incorporated into C. Big Y results.

That makes no sense whatsoever, since FTDNA position is very clear:
Due to the exploratory nature of Big Y, we cannot guarantee results for specific, known SNPs because results will vary from sample to sample. Single specific SNPs are better ordered as such.
The above comes from www.familytreedna.com/learn/y-dna-testing/big-y/big-y/

? ? ?

Mr. W.

P.S.
Paperwork and FF results agree on W. and C. being the 4th cousins.
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  #12  
Old 10th March 2018, 07:57 AM
Jim Barrett Jim Barrett is offline
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Quote:
Originally Posted by dtvmcdonald View Post
I don't understand that. Anybody in my large project can contact anybody else if the ask me for their email.
I hope you don't share the email address without the approval of the kit holder.
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  #13  
Old 10th March 2018, 11:08 AM
The_Contemplator The_Contemplator is offline
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Quote:
Originally Posted by dna View Post
However, the discussion impressed on me that a positive result would not be incorporated into C. Big Y results.
Perhaps whoever was discussing meant, that the Big Y results won't be changed because the single SNP test is a separate thing. Like if a person takes a Big Y and a SNP Pack, the SNP pack results aren't added into the Big Y results/pages. They are separate. They do affect haplogroup if the SNP pack had downstream SNPs that the Big Y did not pick up of course. They would also show up in the haplotree section which is part of the Y-DNA buttons.

Have you tried looking at the VCF of cousin C? Look for the position of the SNP they were not shown results for. It could be that the Big Y did pick it up but in low quantities that they were excluded from Big Y results page.
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  #14  
Old 10th March 2018, 10:20 PM
dna dna is offline
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Quote:
Originally Posted by The_Contemplator View Post
[----] Have you tried looking at the VCF of cousin C? Look for the position of the SNP they were not shown results for. It could be that the Big Y did pick it up but in low quantities that they were excluded from Big Y results page.
I have asked FTDNA for the VCF files.

Mr. W.
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  #15  
Old 11th March 2018, 12:30 PM
wkauffman wkauffman is offline
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Quote:
Originally Posted by dna View Post
W. (me) has a 4th cousin (C.).

Big Y results for C. are missing the final SNP that W., W. grandfather brother, and other men (unrelated to W. or C.) have.

Once that SNP (of BY variety) becomes available for purchase, we will of course order it. However, the discussion impressed on me that a positive result would not be incorporated into C. Big Y results.

That makes no sense whatsoever, since FTDNA position is very clear:
Due to the exploratory nature of Big Y, we cannot guarantee results for specific, known SNPs because results will vary from sample to sample. Single specific SNPs are better ordered as such.
The above comes from www.familytreedna.com/learn/y-dna-testing/big-y/big-y/

? ? ?

Mr. W.

P.S.
Paperwork and FF results agree on W. and C. being the 4th cousins.
One can NEVER expect that two independent samples will provide EXACTLY the same coverage and corresponding calls. If you are looking at a lower quality call and it isn't present as expected in a given sample it comes back to differences in quality and coverage.

FTDNA should NEVER edit in a missing call for a sample based upon other results. The undermines the basic integrity for all of the information which is dependent upon a consistent mechanism for analyzing the data. If individuals were allowed to get calls added back in to results on a case by case basis think of the effect that would have on potential downstream analysis efforts such as age estimation. You skew the statistics with manual edits.
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  #16  
Old 14th March 2018, 06:06 PM
The_Contemplator The_Contemplator is offline
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Quote:
Originally Posted by dna View Post
I have asked FTDNA for the VCF files.
You shouldn't have to ask for the VCF. It is automatically generated. Maybe not available on day one but shortly there after it will be. You need to contact the kit manager to get a copy of it as an admin won't see the link to download it.
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  #17  
Old 14th March 2018, 09:07 PM
dna dna is offline
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Quote:
Originally Posted by The_Contemplator View Post
You shouldn't have to ask for the VCF. It is automatically generated. Maybe not available on day one but shortly there after it will be. You need to contact the kit manager to get a copy of it as an admin won't see the link to download it.
Yes..., thank you, I am all red...

I have logged in as C., and of course everything is there since October.

That particular position I share with my great uncle is not present in C.'s variants.vcf, while that position is within declarations in his regions.bed.


Mr. W.
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  #18  
Old 16th March 2018, 02:10 AM
FuriousGeorge FuriousGeorge is offline
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I'm on yfull now. I'm in V13-S7461-> BY5022*, along with several other people with who'm I share 3 to 13 SNP.

My understanding is that I must have a difference of 30 markers or more with them, as they don't show up on ftdna, and I also understand that each mutation is expected to take 150 years.

If you assume 15 mutations per line to total 30, then that would put the TMRCA at 15 * 150 + your lifetime = ~2300 years.

However, regular TMRCA calculators put the date at around 1200 years, or about half, using conservative settings (30 years per generation, 50% confidence, and ftdna mutation model).

Even if you add some padding for parallel- and back-mutations, you would not expect after 35-50 generation for that to account for a doubling of actual TMRCA. Even a marker with a 2% chance of mutation is not likely to mutate twice in even 50 generations, and slow mutating markers would not be likely to mutate at all.

Would adding 20% or 30% be reasonable?

The age of the branch is estimated at 3700 years. Over previous iterations of the tree it has fluctuated from 4400 to 3300. I think this number is high for us, because we only share 3 SNP with one of the kits there, which would obviously increase that number. Our branch should be split off at some point soon, I assume.

If you disregard that, and count from the other direction (pending uploading a .bam file, and getting a TMRCA based on differing markers), and you consider that from the mutation that defined the branch I share another 13 markers with one kit, that would mean our lines did not split for some time. 150 * 13 + my lifetime = ~2000

3700 - 2000 = 1700 TMRCA


I have 28 novel variants on ftdna, and 24 on yfull. Is it possible ftdna is giving me novel variants that are not really novel, thereby making me more distantly related to the rest of the planet? Non-matching markers upstream of BY5022 should not account, as logically we can all be assumed to have those, and so the result can be inferred if it was ambiguous.

Also, the ftdna snp tree does not really match the yfull tree.

Something /still/ seems broken. Certainly, things are not squaring completely.

Last edited by FuriousGeorge; 16th March 2018 at 02:23 AM.
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  #19  
Old 16th March 2018, 01:31 PM
FuriousGeorge FuriousGeorge is offline
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Quote:
Originally Posted by wkauffman View Post
One can NEVER expect that two independent samples will provide EXACTLY the same coverage and corresponding calls. If you are looking at a lower quality call and it isn't present as expected in a given sample it comes back to differences in quality and coverage.

FTDNA should NEVER edit in a missing call for a sample based upon other results. The undermines the basic integrity for all of the information which is dependent upon a consistent mechanism for analyzing the data. If individuals were allowed to get calls added back in to results on a case by case basis think of the effect that would have on potential downstream analysis efforts such as age estimation. You skew the statistics with manual edits.
I think something went over my head here.

Obviously, users should not be able to send in 3rd party results in order to have their hg changed.

But what if there's an ambiguous result on the terminal branching marker?

(Yfull actually has me in two * HGs, one just downstream of the other. My spot on the tree is based on the upstream marker. No .bam yet, and I don't know if having one will change anything, but I lack reads in what would be my terminal marker. However, I match others on markers it considers downstream of the marker in question.)

As tests improve, I'd think the number of misread markers will go down. Wouldn't that similarly undermine the consistency of the analysis?

If ftdna does the testing, and they're able to clear up an ambiguous situation with a branching marker, why wouldn't that be a good thing?

Perhaps what I'm failing to see is that this person's HG will change anyway, as downstream markers are discovered. That must be the case, otherwise, we're taking the test as the end and not the means, and the snp tree would not reflect reality.

Last edited by FuriousGeorge; 16th March 2018 at 01:37 PM.
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  #20  
Old 28th March 2018, 12:03 PM
buckbeach buckbeach is offline
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Angry BAM availablity

My question is when will BAM become available?

I have recently gotten my Big Y results and have tried to get the BAM link so as to be able to do additional research outside of the FTDNA. Pretty disappointing that after spending the BIG Dollars to get the Big Y (in addtion to the big dollars that I originally spent to get the YDNA-111) that it is no longer provided (for whatever the reason).

I can only suspect that FTDNA is holding back for marketing wanting to sell us more and more SNPs.

BTW, I have purchased for myself: YDA-111, Big Y; mtFullSequence and Family Finder as separate packages over the past several years. I have also purchased recently Family Finders for two 1st cousins and a YDNA 111 for one and a mtFullSequence for the other.

This type of stuff really frustrates me.
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