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View Full Version : BigY Testers consider uploading vcf file to U152 Yahoo group. See below for rationale



MitchellSince1893
06-23-2017, 12:34 AM
Hello,

As some of you know I am an administrator for the FTDNA U152 project and have been asked to encourage interested BigY testers to upload their data to the Yahoo U152 group.

The reason for this post is there is an effort headed up by Iain McDonald to expand his U106 haplogroup dating methodology to include all of P312 as well. Iain's only available source (available to public) for U152 data is the U152 Yahoo group.

Many of you like me have sent your data directly to Alex Williamson for inclusion in his ytree.net, skipping the upload to the U152 yahoo group. Alex cannot share this data with Iain or any other 3rd party because we did not give Alex permission to do so.

In looking at Iain's initial effort, I noticed my branch wasn't included. The reason is because I didn't bother to upload my data to the U152 Yahoo group. I have since done so.

If you would like to be included in this effort then please upload your vcf file to the R1b-U152-Project Yahoo group.

https://groups.yahoo.com/neo/groups/R1b-U152-Project/info


Group Description

The R1b-U152(S28) group's purpose is to advance testing and understanding of U152. This forum is for members of the R1b-U152 project. We share detailed data on U152 haplotypes, relationships and evaluate new SNP discoveries. All U152+ people, including those that are U152+ by default, i.e. L2+, L20+, Z36+, Z56+ are welcome to this group and project. Do not share private data or don't join if concerned.

The location for uploading his https://groups.yahoo.com/neo/groups/R1b-U152-Project/files


Please upload Big compressed VCF file folders (under blue Raw Results button) here. Please add kit #, MDKA surname and date to the file name.

Celt_??
06-23-2017, 01:14 AM
DELETED -

razyn
06-23-2017, 03:15 AM
Deleted this post as it was not specific to U152, and I have no wish to create flak for Mr. Mitchell.

MitchellSince1893
06-23-2017, 05:10 AM
I've uploaded my Big Y data to Alex's Big Tree and YFull. Glad to do this - but what is a MDKA surname? And do you have specific directions beginning from FTDNA results page? You shouldln't assume that we all know exactly where our vcf file is located.
I'm baffled why I'm getting flak for not explaining someone's else's webpage acronym and instructions. I'm not an admin at the U152 Yahoo Group nor am I an FTDNA employee. I'm a volunteer with a full time job and family, who was trying to support someone else's project...but here you go.

MDKA: Most distant known ancestor. FTDNA defines it as "the furthest person who you have documented on a specific genealogical line. In genetic genealogy, it usually refers to someone on a direct maternal line (the mother, her mother, her mother’s mother, etc.) or on a direct paternal line (the father, his father, his father’s father, etc.)

It's the same process you used to upload your BigY data to Alex's BigTree. Here is a screen shot to assist you. Log into FTDNA, go to your BigY page, click on the blue download raw data button, select the vcf file to download to your computer.
17144

join/log into the R1b U152 Yahoo group page, click on the file header...I would tell you more, but at the moment

We're upgrading our systems and some functions of Yahoo! Groups will be unavailable for a few hours. Emails sent to your groups may be delivered late during this time. Thank you for your patience and understanding.

mafe
06-23-2017, 08:30 AM
Do the admins of the U152 project also contact members with new Big-Y results to tell them about further actions they can take (The Big Tree, YFull etc.) ? I am asking this because a Big-Y match within my subclade U152>A274>A275 hasn't popped up yet at 'The Big Tree' or YFull.

Cofgene
06-23-2017, 10:55 AM
Do the admins of the U152 project also contact members with new Big-Y results to tell them about further actions they can take (The Big Tree, YFull etc.) ? I am asking this because a Big-Y match within my subclade U152>A274>A275 hasn't popped up yet at 'The Big Tree' or YFull.

Project admins can go into GAP and download the project's received orders and filter that to get a listing of BigY results within a project. This list can be compared against what has been contributed to various analysis systems to identify missing submissions. Within the U106 region we are missing about 15% of our BigY results. The missing results can be manually mined to establish new clades on FTDNA's tree but that can be a pain to do.

Note that within U106 we are considering a request and method to have FTDNA mail all current U106+ BigY testers. A twist on how GAP email spams occur. IF this moves forward the process could be reused to collect missing BigY files in other haplogroup projects in support of ytree.net and Iain's age analysis efforts.

dp
06-23-2017, 09:07 PM
I have an L2+ kit that has no 37STR panel matches and only 2 25-2's, so I'm hoping to upgrade it Christmas. I'll check to see if I have it in your project.
-dp
PS: Checked. Taylor 443151 kit is in the project.

delegz
06-24-2017, 02:49 PM
I tested with Full Genomes Corp, and my data was successfully uploaded to ytree and yFull. I would be happy to upload my data to the Yahoo U152 group, but I'm not sure what a vcf file is.

Thanks for any insight.


Hello,

As some of you know I am an administrator for the FTDNA U152 project and have been asked to encourage interested BigY testers to upload their data to the Yahoo U152 group.

The reason for this post is there is an effort headed up by Iain McDonald to expand his U106 haplogroup dating methodology to include all of P312 as well. Iain's only available source (available to public) for U152 data is the U152 Yahoo group.

Many of you like me have sent your data directly to Alex Williamson for inclusion in his ytree.net, skipping the upload to the U152 yahoo group. Alex cannot share this data with Iain or any other 3rd party because we did not give Alex permission to do so.

In looking at Iain's initial effort, I noticed my branch wasn't included. The reason is because I didn't bother to upload my data to the U152 Yahoo group. I have since done so.

If you would like to be included in this effort then please upload your vcf file to the R1b-U152-Project Yahoo group.

https://groups.yahoo.com/neo/groups/R1b-U152-Project/info



The location for uploading his https://groups.yahoo.com/neo/groups/R1b-U152-Project/files

MacUalraig
06-24-2017, 03:00 PM
I tested with Full Genomes Corp, and my data was successfully uploaded to ytree and yFull. I would be happy to upload my data to the Yahoo U152 group, but I'm not sure what a vcf file is.

Thanks for any insight.

FGC tend not to hand you a VCF (variant calls) report although they do with their WGS products. You can use a utility to extract one from your BAM file but its better to ask what format of info these guys want - they should be able to take the FGC haplogroup and variantcompare reports.

Solothurn
06-24-2017, 04:08 PM
I have contacted a BigY tester to ask him to join, if he hasn't already that is!

Solothurn
06-24-2017, 04:50 PM
Double post :(

MitchellSince1893
06-24-2017, 04:53 PM
I tested with Full Genomes Corp, and my data was successfully uploaded to ytree and yFull. I would be happy to upload my data to the Yahoo U152 group, but I'm not sure what a vcf file is.

Thanks for any insight.

For version 1 project is only using BigY data. Later version will most likely include data from FGC

MitchellSince1893
06-24-2017, 05:00 PM
Do the admins of the U152 project also contact members with new Big-Y results to tell them about further actions they can take (The Big Tree, YFull etc.) ? I am asking this because a Big-Y match within my subclade U152>A274>A275 hasn't popped up yet at 'The Big Tree' or YFull.

We do not. At present we just don't have the manpower to do this. You may be tempted to think it's just an email, how time consuming is that? That's not the problem. It's the potential of multiple email responses we would get from many of the several hundred BigY test members that we couldn't effectively manage...potentially creating much frustration from our members at not promptly responding. I spent around 3-4 hours this past week researching and answering the questions of a single member. If we open this can of worms with a mass email, we've got to have enough manpower in place to answer responses in a timely and accurate manner. We just aren't there yet.

However, we could add some information about this on the main page. I will discuss with the head admin.

Celt_??
06-24-2017, 06:56 PM
Do the admins of the U152 project also contact members with new Big-Y results to tell them about further actions they can take (The Big Tree, YFull etc.) ? I am asking this because a Big-Y match within my subclade U152>A274>A275 hasn't popped up yet at 'The Big Tree' or YFull.

When I am notified of a new BigY match, I do check it at FTDNA with the link they provide. Then I take personal responsibility to email the few which have zero Non-Matching Known SNPs with me. They usually also have several Shared Novel Variants. I have a standard email which I forward suggesting that they upload their data to Big Y and YFull snd I provide them with links with directions for each. Most of them reply that they have already upload to Big Y, and maybe YFull too. Everyone so far is appreciative.

MitchellSince1893
06-24-2017, 08:36 PM
Found these instructions from Mike W on the R1b-U152 Haplogroup page from back in November 2015


Here is how to get your VCF Zipped file:

Sign in to your myFTDNA account with your kit # (not as a project admin.)

Scroll down until to the OTHER RESULTS section and select the orange BIG Y RESULTS.

On the BIG Y RESULTS screen select the blue DOWNLOAD RAW RESULTS button on the right.

At this point, you may see an error message related to "Houston". If that happens, please check again the next day. It may take a day for FTDNA to update these files.

If you don't get the error message, then just select the green DOWNLOAD .VCF on the left then finally SAVE FILE okay. (Do not select the .BAM file at this point.)

A zipped (compressed) .VCF file folder should download very quickly.

Please rename the file you've downloaded to include the haplogroup, the kit #, paternal line most distant known ancestor (MDKA) surname, and date in following format:

U152_kit999_Surname_BigYRawData_20151105

If you email it to me ([email protected]) I'll upload it to the yahoo group, but you can easily do it yourself. The free storage is under this yahoo group under "FILES". Here is the link: https://groups.yahoo.com/neo/groups/R1b-U152-Project/files/Big%20Y%20results/

Mikewww
06-26-2017, 08:17 PM
Found these instructions from Mike W on the R1b-U152 Haplogroup page from back in November 2015
Here is the URL where the files are stored.

https://groups.yahoo.com/neo/groups/R1b-U152-Project/files/Big_Y_results/

You can upload files directly, just make sure to use the file name format. We particularly need the kit #.

U152_kit999_Surname_BigYRawData_20151105

mafe
06-27-2017, 08:47 AM
We do not. At present we just don't have the manpower to do this. You may be tempted to think it's just an email, how time consuming is that? That's not the problem. It's the potential of multiple email responses we would get from many of the several hundred BigY test members that we couldn't effectively manage...potentially creating much frustration from our members at not promptly responding. I spent around 3-4 hours this past week researching and answering the questions of a single member. If we open this can of worms with a mass email, we've got to have enough manpower in place to answer responses in a timely and accurate manner. We just aren't there yet.

However, we could add some information about this on the main page. I will discuss with the head admin.

Thanks, I appreciate the work you and the other admins are doing. I'll contact my matches and see if they are willing to join YFull and 'The Big Tree'.



When I am notified of a new BigY match, I do check it at FTDNA with the link they provide. Then I take personal responsibility to email the few which have zero Non-Matching Known SNPs with me. They usually also have several Shared Novel Variants. I have a standard email which I forward suggesting that they upload their data to Big Y and YFull snd I provide them with links with directions for each. Most of them reply that they have already upload to Big Y, and maybe YFull too. Everyone so far is appreciative.

I wanted to make sure that the U152-admins hadn't already contacted my matches.

MitchellSince1893
06-27-2017, 05:27 PM
Thanks, I appreciate the work you and the other admins are doing. I'll contact my matches and see if they are willing to join YFull and 'The Big Tree'.
That is fine. Thanks for taking the initiative

There are ongoing discussions on how to get all willing P312 project members (all R1b for that matter) who have done BigY to participate in way that is:

1. Self sustaining. Not dependent on individuals/entities that may not always be around. They are mortals :)
2. Intuitive to the user. Not everyone is computer literate or a native english speaker. What may seem easy to you and I may not be to others.
3. In a format that is helpful and not too manpower intensive/burdensome/risky to the analysts and project admin.

Getting all of these characteristics in a single package is the challenge, but those involved in these discussion are aware of them and are working on an approach that attempts to meet the above criteria. The solution may have a short term approach followed by a long term one.

In the interim, loading your data to the Yahoo U152 group as described in posts 15&16 above will get it to where it needs to be.

MitchellSince1893
07-17-2017, 01:04 PM
FYI: The initial version of this P312 tree with dates may be out by the end of the month. It will contain BigY data loaded to the P312 Yahoo Groups on or before 6 June 2017. Uploads to the Yahoo Groups after this date will appear in the next tree version

Once it's made public the P312 tree and associated dates will be posted here
http://www.jb.man.ac.uk/~mcdonald/genetics.html

MitchellSince1893
07-24-2017, 01:50 PM
FYI: The initial version of this P312 tree with dates may be out by the end of the month. It will contain BigY data loaded to the P312 Yahoo Groups on or before 6 June 2017. Uploads to the Yahoo Groups after this date will appear in the next tree version

Once it's made public the P312 tree and associated dates will be posted here
http://www.jb.man.ac.uk/~mcdonald/genetics.html

P312 and subclade dates are up. http://www.jb.man.ac.uk/~mcdonald/genetics.html

Here is the direct P312 date link below

Clade Best guess (95% confidence interval)
P312 3155 BC (3898 BC — 2568 BC)
DF19 2747 BC (3596 BC — 1773 BC)
U152 2737 BC (3320 BC — 2233 BC)
DF27 3028 BC (3741 BC — 2423 BC)
L21 2934 BC (3638 BC — 2362 BC)
http://www.jb.man.ac.uk/~mcdonald/genetics/p312/table.html

Keep in mind this is version 1.0. Much data has come in since the 6 Jun 2017 cut off for this version. So expect things to adjust a little in the next version.

NOTE: Unless manually entered, only SNPs found in the BigY vcf files will be listed in the P312 section. Also future versions may take into account ancient dna dates. E.g. RISE563 U152 is dated to 2572-2512 BC so that would affect the U152 date range.

A.Morup
07-25-2017, 07:32 AM
If you do not wish to create a Yahoo profile, is there any way to contribute with your VCF-file?

MitchellSince1893
07-25-2017, 12:45 PM
If you do not wish to create a Yahoo profile, is there any way to contribute with your VCF-file?

Please rename the file before you upload it with your major subclade, the kit number, MDKA surname and date of the file in a format similar to this:

L2_N54638_Walsh_BigY_RawData_2 0170626.zip

Sending it mikewww at [email protected] to upload is your acknowledgement that you are sharing your kit, MDKA and results (not your personal contact info) for the analysis. There are no charges for the analysis. This is all volunteer work.

A.Morup
07-25-2017, 02:24 PM
Thanks!
But I already sent the file for Mike for the great Ytree a year ago.
Does he need it again then? Maybe acknowledgement that McDonald can also use it?

MitchellSince1893
07-25-2017, 02:58 PM
Thanks!
But I already sent the file for Mike for the great Ytree a year ago.
Does he need it again then? Maybe acknowledgement that McDonald can also use it?

I think so. You can contact him directly to confirm. Specify it is for the U152 Yahoo group.

Cofgene
07-25-2017, 03:34 PM
Thanks!
But I already sent the file for Mike for the great Ytree a year ago.
Does he need it again then? Maybe acknowledgement that McDonald can also use it?

Yes, it needs to be resent. This is a privacy protection issue. The data that was contributed to Ytree could be interpreted as being provided only to that individual/effort. With the data being uploaded into a public haplogroup repository it is clearer that the data is being openly contributed for a number of analysis efforts. We want to avoid having backdoor data transfers between various analysis efforts occurring which could lead to legal issues and potential additioinal data controls from providers such as FTDNA so they can cover their butts from lawyers.

A.Morup
07-26-2017, 07:59 AM
Done! Thanks to both of you :-)