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REWM
10-21-2017, 04:01 PM
19395

YFull has a new feature for Verified novel SNPs by Sanger sequencing with YSEQ. I think it can be useful in verifying if it's legit or with someone who has not did NGS testing. I would like to see it added to known SNPs for use with NO Calls. I know it would be very helpful in my Z2573 group where by it's not covered in Big Y along with other known SNPs. If YFull can accept these verified results it would be a good way for expanding the Y tree. In my case I was able to prove a split in my line of A6104 by testing my novel FGC32106 and and a man who has A6266 which both are listed as a novel. Unfortunately neither of these SNPs are testable at FTDNA.

REWM
10-30-2017, 04:33 PM
A good blog post on Big Changes to YFull.

https://ultimatefamilyhistorians.blogspot.com/2017/10/big-changes-to-yfull.html

JamesKane
10-30-2017, 05:31 PM
The feature is a little mis-informative. What is happening is they are displaying the testing summary for the location from the YBROWSE data dump. Since there isn't a link for the YFULL id and YSEQ id(s) that have tested for the SNPs, it's not really validated by Sanger sequencing. All this is really telling you the location can be Sanger sequenced at YSEQ.

YFULL could implement this by creating a project at YSEQ for everyone to join and then allowing us to add the YSEQ id similar to how you can add your FTDNA id.

gotten
10-30-2017, 05:45 PM
The feature is a little mis-informative. What is happening is they are displaying the testing summary for the location from the YBROWSE data dump. Since there isn't a link for the YFULL id and YSEQ id(s) that have tested for the SNPs, it's not really validated by Sanger sequencing. All this is really telling you the location can be Sanger sequenced at YSEQ.

Ha, I was wondering what it really symbolized. So REWM's result can be derived from here (http://ybrowse.org/gb2/gbrowse_details/chrY?ref=chrY;start=12366071;end=12366071;name=FGC 32106;class=Sequence;feature_id=283913;db_id=chrY% 3Adatabase), with count_derived and count_tested as the important variables in the Yfull tooltip.

I assume you mean this (http://ybrowse.org/gbrowse2/gff/) with Ybrowse data dump?

REWM
10-30-2017, 05:51 PM
That's true, but for me it was validated by YSEQ within the Z2573 group there. I hope YFull does so in the near future.

REWM
10-30-2017, 05:53 PM
I think he means this. There yseq groups.


https://www.yseq.net/group_browser.php?osCsid=edb9d3013e53e6faef170ba3e d8640ae

JamesKane
10-30-2017, 05:59 PM
I assume you mean this (http://ybrowse.org/gbrowse2/gff/) with Ybrowse data dump?

That's correct. They have to import that repository from time to time to get new names assigned to variants anyway, so it's just putting some of the meta-data to work here.

ljonas1
11-06-2017, 12:25 AM
The new "Verified by Sanger sequencing" icon at YFull indicates more than "this location is available for Sanger sequencing," but maybe less than "verified." If it meant "this location is available for Sanger sequencing," then almost every high quality, acceptable quality, ambiguous quality, and low quality SNP in my brother's test results would show this icon because I have submitted them all to YSeq (YSeq rejected a couple of them). What it indicates is that the location is not only available for testing, but that someone has actually been tested there. Of course, it is not truly "verified" until someone tests positive for it. I show two examples in my blog post "Big changes to YFull." In the first example one person tested negative. This SNP is not truly "verified." The other SNP belonging to REWM was verified.