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

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  #1  
Old 28th August 2017, 09:44 AM
LarryBurford LarryBurford is offline
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Join Date: Jun 2015
Posts: 190
Who to test on Big Y

If I were to do a Big Y test who should I upgrade and would it matter. I have my Dad, Myself and my son all on FTDNA. Would it be better to test my dad the oldest or my son the youngest? My guess is that it would not matter but I wanted to hear from some experts.

Larry
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  #2  
Old 28th August 2017, 10:57 AM
ech124 ech124 is offline
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Join Date: Jul 2011
Posts: 209
All three will match very closely.

If it were me, I would test the father. He is the one closest to the "origin" if you are trying to trace your roots. There is a small chance that mutations have occurred in your family even within the last several generations. The chances are slight, but you can avoid that by testing the oldest individual. Also you have the advantage of the DNA being stored (if it isn't already) and that opens the option of post-death testing. The odds are the oldest in the family will pass away first and you want to keep your testing options open especially if new DNA methods appear with future technology advancements.
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  #3  
Old 27th September 2017, 08:08 AM
A.Morup A.Morup is offline
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Join Date: Feb 2016
Posts: 18
The son!

If not too late, then test your son - he will have the maximum of novel SNPs (+2 generations from your father). You can always test your father and yourself for your son's novel SNPs at Yseq.net afterwards and see if he/you have them too. You can not do the opposite!
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  #4  
Old 1st October 2017, 06:57 PM
JSW JSW is offline
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Join Date: Apr 2003
Location: San Antonio, TX
Posts: 313
Another thing to keep in mind is you may have to test
two (mayber more?) men with Big-Y to get a consensus on some SNPS
Here is my story.
I have a Big-Y test along with a cousin (different surname
due to a 1756 orphan NPE) We have an STR match at 111
along a family finder atDNA match. He is a 5th cousin.

Per FTDNA we do NOT have a Big-Y match. So I decided to have my brother tested.
Thus I now have Me(M) Brother(B) and Cousin(C) results
from FTDNA web site
On the compare page M vs B is in position 11 there are
ten above us.
Compare results:
We are all R-z2563 with over 400 Big-Y matches
M vs B 2 Non-matching known SNPs M367 L362 Shared Novel 35
M vs C No Match
B vs C 3 Non-matching known SHPs Z2001,L1008,L1089 Novel 33

It is my theory that FTDNA test got All or most of those
5 SNPs wrong in my results. That would give me
a "Non-Matching Known SNP" difference of 5 between M & C which is why M does
not match C on the FTDNA web pages.
I think the best way to look at matches is to sort them
on descending Shared Novel Variants.
NOT on ascending Known SNP difference as FTDNA default page show it.
Any others with thoughts on this?
Do we have any data on the possible rate of false calls in the Big-Y results?
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  #5  
Old 1st October 2017, 08:53 PM
rivergirl rivergirl is offline
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Join Date: Jul 2006
Posts: 791
JSW, Have you had the 3 Big Y results analysed by Yfull or FGC. Or Alex Wiliamson if your R-L21.
They usually do a better job than FTDNA.
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  #6  
Old 2nd October 2017, 10:12 AM
JSW JSW is offline
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Join Date: Apr 2003
Location: San Antonio, TX
Posts: 313
Re Outside FTDNA analysis
My kit has been analyzed by YFULL the other two have
not -that is on my longer term "to do" list

Yesterday I downloaded the list of Novel Variants for the
three kits. There are 35 for each for each.
The compare shows the following:
The three kits have 31 Novel Variants in common
Cousin kit has 2 SNPs not in the other two
Cousin Kit has 1 SNP in Brother not in my kit.
Cousin kit has 1 SNP in my kit not in Brother
Brother and my kit have 3 SNPs not in Cousin.

FTDNA only reports novel variants that are of
"High" Confidence level.
That tells me we do know know for sure about the
mismatches. For example in this case:
Cousin Kit has 1 SNP in Brother not in my kit.
Is the SNP in question in my data recorded
with "Reference" value and "High" confidence
Or could it just be the confidence is not "High"
and thus not reported?
I will have to look at the other files to see.
I do not know if that is in the VCF file
or not I know it is in the BAM file
and I have that so I will be able to
review that one SNP and report back here.
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  #7  
Old 28th November 2017, 07:20 PM
mlcarson mlcarson is offline
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Join Date: Jan 2017
Posts: 77
I've got the same question. I've tested myself and a maternal uncle via Big-Y. I've done FF and MTFull on my father but no Y-testing since I expected the results to be identical to my own. I'm just wondering that since there's a sale going on whether it would be worth doing a Y-12 and a Big-Y on my father. This testing would get me a free upgrade to Y-111 and I'd have Big-Y for the additional STR values that they'll be doing next year but is there any value in it? My gut feeling is that there isn't because the testing will probably show the exact same results for both tests.

My thoughts at the moment are that FF tests for more people are the best use of funds.
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  #8  
Old 29th November 2017, 12:45 AM
JSW JSW is offline
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Join Date: Apr 2003
Location: San Antonio, TX
Posts: 313
I have yet to get my Big-Y back after the Oct 10 up grade.
But before that Big-Y between myself and my brother showed
3 SNP differences
There may be some value in father/son test in the old system
I wish I could tell you how it is now.
My brother's test came back 4 week ago
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  #9  
Old 29th November 2017, 04:02 PM
dtvmcdonald dtvmcdonald is offline
mtDNA: | Big Y Pending
 
Join Date: Mar 2011
Posts: 220
Quote:
Originally Posted by JSW View Post
Any others with thoughts on this?
Do we have any data on the possible rate of false calls in the Big-Y results?
Its very small compared to 10 million, or the current
300,000 or so on their list.

In my project we are averaging 6 bogus SNPs listed as
Novel Variants for each person. That's a huge average
as far as matching goes.

We are averaging 4 bad known SNPs per person. However,
some are more.

These are usually above 50,000,000, in the centromere,
or inside STRs or pseudo STRs.

In other words, they've got problems.

There seem to be patterns in this however ... which means
that the patterns themselves may actually be reliable!

I've found 3 very reliable structural variants by examining
bogus SNP patterns. These determine a very important clade, and even better, they can be RELIABLY measured using the new VCF files! To do this you need lots of test results with BAM files to stare at (VCFs and the online browser would not have done the trick.)

************************************************** **

Two VERY important new BigYs appeared today with piles and
piles of bad SNPS and three very useful, very important new SNPs
on each.
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