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

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  #1  
Old 15th October 2017, 01:57 PM
mwwalsh mwwalsh is offline
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Join Date: Oct 2007
Posts: 152
Big Y enhancements started Oct 10th

My Big Y results have not been updated yet so I can't much of this. There are a number of enhancements in Big Y. The new Big Y results will all be using the updated reference model Hg38. Think of it as a map that the Big Y most raw results are compared with to to look for changes (variants or SNPs).

It's more complicated but I don't know if everyone wants all the details or cares. All prior Big Y results are supposed to be converted to the Hg38 format. This is important so comparisons can be apples to apples. This the essence of discovering the tree branching in genetic genealogy.

There new and improved on-line tools that make analysis easier for more people. There is Big Y Chromosome Browser and an Terminal SNP Guide has been added to the Big Y Matching. This is important as the old way was very limited.

If interested, please become familiar with the Big Y Learning Center.

https://www.familytreedna.com/learn/...g/big-y/big-y/
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  #2  
Old 15th October 2017, 02:57 PM
dtvmcdonald dtvmcdonald is offline
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Posts: 264
If the new Build 38 pages that have appeared are any guide
to what will happen after all are converted, there is still totally insufficient info to be sure of generating a correct
tree of people. One will still need BED files at the very least, and in some cases BAM files too, as the chromosome browser does not give read map quality info. That's important.

Based on how many updated web pages have appeared so far,
I calculate that the update will take 80 days.
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  #3  
Old 15th October 2017, 03:13 PM
mwwalsh mwwalsh is offline
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Quote:
Originally Posted by dtvmcdonald View Post
If the new Build 38 pages that have appeared are any guide
to what will happen after all are converted, there is still totally insufficient info to be sure of generating a correct
tree of people. One will still need BED files at the very least, and in some cases BAM files too, as the chromosome browser does not give read map quality info. That's important.
It appears that the VCF files are much more robust in providing quality of the test call per location but they may not include locations with less that 4x reads.

The Big Y Chromosome Browser needs to support going directly to a specified location, even if it has less that 4x reads.... in my opinion. Otherwise, we have to go through all the BAM rig-a-ma-roll stuff anyway or at least down at the real genetic genealogy levels of the last several hundred years.

Dtvmcdonald, are you of the opinion that if there is a no derived call in the VCF and the location is within a BED region we can reliably assume it is truly ancestral? We've had luck with that in past analyses but it is sometimes wrong. With greater reporting down to 4x maybe in the VCF files maybe that just about solves the problem. Maybe not.

What's the qualifications for BED regions inclusion? Is FTDNA including locations with only 4x coverage? I don't know. I can probably live with that, but there will be cases where external BAM interpretations are needed anyway unless FTDNA allows one to go a specific location on the Big Y Browser.

Quote:
Originally Posted by dtvmcdonald View Post
Based on how many updated web pages have appeared so far,
I calculate that the update will take 80 days.
I don't know if it will take that long, but it is going slower than I thought. I thought it was 5-7 days so we shall see how much progress is made by about Wednesday.

In any case, I can easily see it taking 80 days of kinks to work out.

Last edited by mwwalsh; 15th October 2017 at 03:22 PM.
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  #4  
Old 15th October 2017, 07:44 PM
The_Contemplator The_Contemplator is offline
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The "New Big Y Results" email sent by FTDNA is outdated. It uses the old (no longer existing) Big Y learning center page link among other outdated details. I reported it to FTDNA and I was told the following earlier today (Sunday).

Quote:
We are going through a Big Y update right now. Big Y 2.0 will be completed by the end of next week.
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  #5  
Old 15th October 2017, 08:33 PM
mwwalsh mwwalsh is offline
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Quote:
Originally Posted by The_Contemplator View Post
The "New Big Y Results" email sent by FTDNA is outdated. It uses the old (no longer existing) Big Y learning center page link among other outdated details. I reported it to FTDNA and I was told the following earlier today (Sunday).
I'm not sure what link is the old link or whatever but I received by email on Thursday from the FTDNA project admin help desk this URL:
https://www.familytreedna.com/learn/...g/big-y/big-y/

It looks relevant as it talks about the new SNP Terminal Guid and new Big Y on-line Browser.
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  #6  
Old 15th October 2017, 10:05 PM
The_Contemplator The_Contemplator is offline
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Right. I'm aware of the new one. The old one is this one:
http://www.familytreedna.com/learn/u...ts/big-y-page/
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  #7  
Old 19th November 2017, 07:44 AM
phobrla phobrla is offline
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Join Date: Jul 2016
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Results Pending...until Jan 2018?

Currently I'm not seeing any matches; all of my old matches are gone. I do, however, have access to the New UI for Big-Y and it shows that it was processed on October 27. Should I expect not to have updated Matches until sometime in January 2018, then?

Quote:
Originally Posted by dtvmcdonald View Post
Based on how many updated web pages have appeared so far,
I calculate that the update will take 80 days.
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  #8  
Old 19th November 2017, 12:02 PM
The_Contemplator The_Contemplator is offline
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Your previous matches may have been too distant to be meaningful matches. FTDNA has changed the matching limits and this would explain why many matches do not appear. However, they are still messing with the update and it is possible they tweak things that cause some matches to appear. We simply don't know at this moment.
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  #9  
Old 21st November 2017, 03:33 PM
phobrla phobrla is offline
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Quote:
Originally Posted by The_Contemplator View Post
Your previous matches may have been too distant to be meaningful matches. FTDNA has changed the matching limits and this would explain why many matches do not appear. However, they are still messing with the update and it is possible they tweak things that cause some matches to appear. We simply don't know at this moment.
That would be in line with my Y-Full results then...
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  #10  
Old 21st November 2017, 09:41 PM
The_Contemplator The_Contemplator is offline
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You could try to convince your best STR matches to get the Big Y. Let them know about the sale (assuming they don't pay attention to the FTDNA emails) and that they get a free upgrade to Y111 if they get it during the sale.

For one of the kits I managed, there were no close matches. I have since managed to talk 9 others to take the Big Y.
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