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Thread: Y DNA Data Warehouse - accepting Big Y VCF files

  1. #1
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    Lightbulb Y DNA Data Warehouse - accepting Big Y VCF files

    Good news, a person from the old S1194 (and CTS4528) project has worked out a deal to have the Alex Williamson Big Tree and Iain McDonald Age Estimates methods worked for this subclade. He announced this today on the Big Y FB forum. This is just a natural extension of what is already being done for P312 and U106, which are brothers to S1194 under R1b-L151.

    This is a volunteer service (no fees). If you are a Big Y tester and want to engage in this please submit your information using the following instructions.

    Bring up James Kane's Y DNA Data Warehouse submission form in one window:
    http://www.haplogroup-r.org/submit_data.php

    Fill in the FTDNA kit# and make sure the correct Human Reference Build is selected.

    Fill in the Most Distant Known Male Ancestor information that you are comfortable sharing. Please remember, only the Surname and year of birth should be provided. We will provide the ability to provide more details privately for genealogical matching in the future.

    Log into your FTDNA account in a second browser window and navigate to the Big Y results page.

    Click the "Download Raw Data" button to open the download screen.

    Right click (or hold down the Control key while clicking on a Mac) the "Download VCF" button. This will show a context menu of choices.
    Choose the "Copy Link" menu item.

    Paste the link into the "Download URL" box of the submission form.

    The Y DNA Data Warehouse is also a volunteer service and is accepting VCF zipped folders (copy/paste links) for other parts of haplogroup R even though there are no applications supporting the other haplogroups yet. Please contact Alex Williamson if you have technical skills are interested in using his Big Tree web user interface.

    They set up a stub for R1b-M269 but not much is being done with this yet, although now it looks like all of R1b-L151 is basically covered.

    http://www.ytree.net/DisplayTree.php?blockID=924

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  3. #2
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    Mike,

    If Alex already included me in his tree based on the hg19 vcf file, does it make sense to upload the new hg38 file to the Y DNA Data Warehouse?

    Upon conversion, I only "gained" about 6 new, really low quality SNP's.

    Regards

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    Quote Originally Posted by Menchaca View Post
    Mike,

    If Alex already included me in his tree based on the hg19 vcf file, does it make sense to upload the new hg38 file to the Y DNA Data Warehouse?

    Upon conversion, I only "gained" about 6 new, really low quality SNP's.

    Regards
    I resubmitted for both of my Big Y kits. There are advantages to the Hg38 reference model that allow FTDNA to make higher confidence variance calls. There are some new SNPs being found but that is not common. However, the confidence in calls and also the confidence then the resulting trees and SNP age estimates should be improved.

    Beyond that, the new VCF files are much, much more robust. In reality, the old VCF files did not provide much information, which is partially why the BAM files were very important. BAM files are still important, but will be reveal less additional information relative to the new, robust VCF files. If you download your new VCF and compare it with your old you will see what I mean. This is why we need this data warehouse. Yahoo groups will not support the size of the files that VCFs now are.

    When we talk about quality we should separate out the difference between a variant that is unstable or in an unstable region of the Y chromosome versus and low quality test "call".

    If you are anything in R1b-L151, be it any part of P312, U106 or their smaller brother, S1194 (CTS4528), you will be placed on two of the applications that use the Y DNA Data Warehouse as their source for data. Those two are the Williamson Big Tree and the McDonald SNP Age Estimates.

    There are plans for future applications too and broader haplogroup coverage. If you are interested the right person to contact is James Kane.
    Last edited by TigerMW; 01-19-2018 at 09:57 PM.

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  6. #4
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    Is McDonald estimating the age of P312 SNPs? If so, can you provide a link? Is there another source for this besides Full?
    Last edited by GoldenHind; 02-07-2018 at 12:10 AM.

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    Quote Originally Posted by GoldenHind View Post
    Is McDonald estimating the age of P312 SNPs? If so, can you provide a link? Is there another source for this besides Full?
    Some of the estimates are at the bottoms of the Big Tree reports. Scroll to the bottom of this page for example:
    http://www.ytree.net/BlockInfo.php?blockID=836
    R1b>M269>L23>L51>L11>P312>DF19>DF88>FGC11833 >S4281>S4268>Z17112>BY44243

    Ancestors: Francis Cooke (M223/I2a2a) b1583; Hester Mahieu (Cooke) (J1c2 mtDNA) b.1584; Richard Warren (E-M35) b1578; Elizabeth Walker (Warren) (H1j mtDNA) b1583;
    John Mead (I2a1/P37.2) b1634; Rev. Joseph Hull (I1, L1301+ L1302-) b1595; Benjamin Harrington (M223/I2a2a-Y5729) b1618; Joshua Griffith (L21>DF13) b1593;
    John Wing (U106) b1584; Thomas Gunn (DF19) b1605; Hermann Wilhelm (DF19) b1635

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    Quote Originally Posted by GoldenHind View Post
    Is McDonald estimating the age of P312 SNPs? If so, can you provide a link? Is there another source for this besides Full?
    Yes

    http://www.jb.man.ac.uk/~mcdonald/ge...312/table.html
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    Hidden Content

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