|
Hi folks,
Just a note for those who have participated in the past, the YDNA Warehouse is now importing Big Y STR CSVs beyond the 111 marker panels. ?We will be using these to compute the ancestral values at each tree branch and adding them to the . ?Currently, 8 of the 374 of you who have provided a BAM have also added the STR file with extended values.
CSV files are uploaded to a FTDNA STR or SNP Panel kit under your test Subject.
If the row above already exists click the Manage button, and follow the instructions at the bottom of the page.
And finally... the updates. ?I have successfully realigned the 374 BAMs already in my possession to the telomere-to-telemore reference, CHM13 and HG002, being internally piloted by FTDNA's?G?ran Runstr?m. ?These samples along with 1000 other fairly random ones are running through??to begin constructing a tree using this data. ?As new potential branches are found under CTS4466, I'll share my findings here.
?also has access to the VCF and coverage BED files for this new accession. ?Hopefully, you'll be able to see new updates show up there as well.
As always if you have trouble getting logged in or finding where to start send me a note directly by email. ?We'll get you sorted out.
Thanks,
James Kane
PS: ?I plan to consolidate the STR, Big Y-500 and Big Y-700 tests into a single test unit in the future. ?This will bring us more inline with how you all are used to a Big Y-700 being the test that gives you STRs these days at FTDNA.
|
James, ? Amazing progress, as your interventions always are! As you are aware I have been indicating postulated ancestral values at each tree branch on my Irish Type II / CTS4466 (and other haplogroup) trees all along, and since 2019 for several these trees have included the 727 markers for which FTDNA extracts data from Big Y tests. Apart from downloading the .csv files to a single massive spreadsheet, my methods are laboriously non-computerised, I.e. mutations are identified by visual inspection of the data. I recognise that universal application of such analysis needs a method such as yours. ? Since I use the output from this exercise to estimate the age at each tree branch it is important that my identification of mutations is close to being correct. ? I’m sure that comparison with your YDNA Warehouse results will cause me to rethink placement of some of the mutations I have postulated. I am equally sure that I will argue, based on logic rather than your program, that some of your conclusions cannot be correct. Will you have an override facility which can be applied if you are in agreement with me (if ever you have time to review such cases in depth!)? ? My own work has identified a number of independent levels on the trees which are defined solely by STR mutations, as would be expected. A few of these, early on, are particularly significant (e.g. FTY1172 on sheet 5 of the Irish Type II tree).Will the Warehouse trees have similar characteristics, or will STR mutations only be marked as coincident with SNPs? ? (I still await a response from Michael Sager to comments on FTDNA’s mew ‘Discovery’ tree node age estimates). ? Nigel Sent from for Windows ?
toggle quoted message
Show quoted text
From: James KaneSent: 15 July 2022 23:22 To: [email protected]Subject: [R1b-CTS4466-Plus] YDNA Warehouse STR Uploads and Updates ? Hi folks,
Just a note for those who have participated in the past, the YDNA Warehouse is now importing Big Y STR CSVs beyond the 111 marker panels. ?We will be using these to compute the ancestral values at each tree branch and adding them to the . ?Currently, 8 of the 374 of you who have provided a BAM have also added the STR file with extended values.
CSV files are uploaded to a FTDNA STR or SNP Panel kit under your test Subject. 
If the row above already exists click the Manage button, and follow the instructions at the bottom of the page. 
And finally... the updates. ?I have successfully realigned the 374 BAMs already in my possession to the telomere-to-telemore reference, CHM13 and HG002, being internally piloted by FTDNA's?G?ran Runstr?m. ?These samples along with 1000 other fairly random ones are running through??to begin constructing a tree using this data. ?As new potential branches are found under CTS4466, I'll share my findings here.
?also has access to the VCF and coverage BED files for this new accession. ?Hopefully, you'll be able to see new updates show up there as well.
As always if you have trouble getting logged in or finding where to start send me a note directly by email. ?We'll get you sorted out.
Thanks,
James Kane PS: ?I plan to consolidate the STR, Big Y-500 and Big Y-700 tests into a single test unit in the future. ?This will bring us more inline with how you all are used to a Big Y-700 being the test that gives you STRs these days at FTDNA.
|
how do i provide a BAM if that is needed?
dave
|
Checking if the warehouse has the BAM: 1) Log in to YDNA Warehouse and click the Manage button on the test Subject. 2) Find the Big Y test kit data and click the Manage button. ?You will see a screen like this.  3) If you see any file called chrY.bam, chrYM.cram or callable_status.bed, you are good! ?No action is needed. The BAM/CRAM file just might not be re-uploaded yet. If you only see the files pictured above, a BAM file hasn't been submitted. 4) Open your FTDNA account in another browser window and navigate to your Big Y results page. 5)?Click the blue Download Raw Data button. This will open a modal dialog box with a privacy information statement. 6)?Click the green Share button to access a file download URL token. 7)?Copy the token into the "Retrieve file from Cloud service" box. The link will be nearly 500 characters long. 8) Click the Retrieve file button. The BAMs are typically processed in 72 hours and this page gets some additional tabs with analysis information. Thanks for the question. James Kane PS: ?If you have one of those very long Kit# as shown above and would prefer having your FTDNA kit # there message me directly with what it should be changed to.
|
Will you have an override facility which can be applied if you are in agreement with me (if ever you have time to review such cases in depth!)? Yes, eventually. ?I am on and off working on a set of editing tools for the tree. ?Each branching block notes the changes from its parent block. ?The state changes can be SNPs, INDELs or STRs. ? ?Way down the road I’d also like to include a concept like a person as well for proven lineages. ?The state changes can be redefined manually in the report that renders the tree in your browser.
The intent is to allow a team to fix the tree’s mistakes and make further refinements manually.
Will the Warehouse trees have similar characteristics, or will STR mutations only be marked as coincident with SNPs? Yes, covered by the above functionality. ?A new Block with the STR mutation could be inserted between existing SNP block. ?I already do this with INDELs , since including them is an NP-hard problem for the current machine learning solutions.
Thanks,
James
|
Hi, ? I manage my deceased father’s DNA and had the Big Y DNA performed. His name is Richard McAvoy. I am not sure what results you have. I do not know what a BAM is and if you have my father's BAM. I have attached the his Big Y STR CSV.? Thanks, Marcia McAvoy
On Jul 15, 2022, at 6:22 PM, James Kane <jkane@...> wrote:
? Hi folks,
Just a note for those who have participated in the past, the YDNA Warehouse is now importing Big Y STR CSVs beyond the 111 marker panels. ?We will be using these to compute the ancestral values at each tree branch and adding them to the . ?Currently, 8 of the 374 of you who have provided a BAM have also added the STR file with extended values.
CSV files are uploaded to a FTDNA STR or SNP Panel kit under your test Subject.
If the row above already exists click the Manage button, and follow the instructions at the bottom of the page.
And finally... the updates. ?I have successfully realigned the 374 BAMs already in my possession to the telomere-to-telemore reference, CHM13 and HG002, being internally piloted by FTDNA's?G?ran Runstr?m. ?These samples along with 1000 other fairly random ones are running through??to begin constructing a tree using this data. ?As new potential branches are found under CTS4466, I'll share my findings here.
?also has access to the VCF and coverage BED files for this new accession. ?Hopefully, you'll be able to see new updates show up there as well.
As always if you have trouble getting logged in or finding where to start send me a note directly by email. ?We'll get you sorted out.
Thanks,
James Kane
PS: ?I plan to consolidate the STR, Big Y-500 and Big Y-700 tests into a single test unit in the future. ?This will bring us more inline with how you all are used to a Big Y-700 being the test that gives you STRs these days at FTDNA.
|
James, Both of my cousins have done the Big-Y DNA. I'm not sure if I sent the raw data to you or if you need it?? Gordon Shuckrow, Jr. (FTDNA kit #424423) William Chance Shuckrow (FTDNA kit #MK66026)
I've also been in contact with Michael Power (adopted) and his bio dad John Sugrue, Sr. of County Cork, Ireland. They have both done FT Y67-DNA that is a match at one distance to Gordon Shuckrow. Unfortunately, Michael died unexpectedly from cancer but his bio dad is still alive. I'm in contact with Michael's widow.
Please advise if I need to do anything now, Sue
On Fri, Jul 15, 2022 at 3:22 PM James Kane < jkane@...> wrote: Hi folks,
Just a note for those who have participated in the past, the YDNA Warehouse is now importing Big Y STR CSVs beyond the 111 marker panels.? We will be using these to compute the ancestral values at each tree branch and adding them to the .? Currently, 8 of the 374 of you who have provided a BAM have also added the STR file with extended values.
CSV files are uploaded to a FTDNA STR or SNP Panel kit under your test Subject.
If the row above already exists click the Manage button, and follow the instructions at the bottom of the page.
And finally... the updates.? I have successfully realigned the 374 BAMs already in my possession to the telomere-to-telemore reference, CHM13 and HG002, being internally piloted by FTDNA's?G?ran Runstr?m.? These samples along with 1000 other fairly random ones are running through??to begin constructing a tree using this data.? As new potential branches are found under CTS4466, I'll share my findings here.
?also has access to the VCF and coverage BED files for this new accession.? Hopefully, you'll be able to see new updates show up there as well.
As always if you have trouble getting logged in or finding where to start send me a note directly by email.? We'll get you sorted out.
Thanks,
James Kane
PS: ?I plan to consolidate the STR, Big Y-500 and Big Y-700 tests into a single test unit in the future.? This will bring us more inline with how you all are used to a Big Y-700 being the test that gives you STRs these days at FTDNA.
-- Enjoy a great day, Sue Severson 67 Martha Road, Orinda, CA 94563
925-255-7570
|
Hi Nigel, Phil Millar (PJRM) here - FTDNA Kit No: B654981?-
an Admin, with my permission, when I was first joining projects, uploaded my file to the YDNA Warehouse, my Haplogroup is R-BY186342 but I think they've got me as an upstream subclade R-A6526, my family we're from Ulster (Northern Ireland) Antrim. Nigel, do
you have access to my file at YDNA Warehouse, if you don't, do I need to enable something, so you can? Nigel, just let me know what I need to do, to help you. Adh mor ort agus oiche mhaith.
Phil
toggle quoted message
Show quoted text
James,
?
Amazing progress, as your interventions always are! As you are aware I have been indicating postulated ancestral values at each tree branch on my Irish Type II / CTS4466 (and other haplogroup) trees all along, and since 2019 for several these trees have included
the 727 markers for which FTDNA extracts data from Big Y tests. Apart from downloading the .csv files to a single massive spreadsheet, my methods are laboriously non-computerised, I.e. mutations are identified by visual inspection of the data. I recognise
that universal application of such analysis needs a method such as yours.
?
Since I use the output from this exercise to estimate the age at each tree branch it is important that my identification of mutations is close to being correct.
?
I’m sure that comparison with your YDNA Warehouse results will cause me to rethink placement of some of the mutations I have postulated. I am equally sure that I will argue, based on logic rather than your program, that some of your conclusions cannot be correct.
Will you have an override facility which can be applied if you are in agreement with me (if ever you have time to review such cases in depth!)?
?
My own work has identified a number of independent levels on the trees which are defined solely by STR mutations, as would be expected. A few of these, early on, are particularly significant (e.g. FTY1172 on sheet 5 of the Irish Type II tree).Will the Warehouse
trees have similar characteristics, or will STR mutations only be marked as coincident with SNPs?
?
(I still await a response from Michael Sager to comments on FTDNA’s mew ‘Discovery’ tree node age estimates).
?
Nigel
Sent from for Windows
?
?
Hi folks,
Just a note for those who have participated in the past, the YDNA Warehouse is now importing Big Y STR CSVs beyond the 111 marker panels. ?We will be using these to compute the ancestral values at each tree branch and adding them to the
. ?Currently, 8 of the 374 of you who have provided a BAM have also added the STR file with extended values.
CSV files are uploaded to a FTDNA STR or SNP Panel kit under your test Subject.
If the row above already exists click the Manage button, and follow the instructions at the bottom of the page.
And finally... the updates. ?I have successfully realigned the 374 BAMs already in my possession to the telomere-to-telemore reference, CHM13 and HG002, being internally piloted by FTDNA's?G?ran Runstr?m. ?These samples along with 1000 other fairly random ones
are running through??to begin constructing a tree using this data. ?As new potential branches are found under CTS4466, I'll share my findings here.
?also has access to the VCF and coverage BED files for this new accession. ?Hopefully, you'll be able to see new updates show up there as well.
As always if you have trouble getting logged in or finding where to start send me a note directly by email. ?We'll get you sorted out.
Thanks,
James Kane
PS: ?I plan to consolidate the STR, Big Y-500 and Big Y-700 tests into a single test unit in the future. ?This will bring us more inline with how you all are used to a Big Y-700 being the test that gives you STRs these days at FTDNA.
|
Hi Nigel, Phil Millar (PJRM) here - FTDNA Kit No: B654981?- an Admin, with my permission, when I was first joining projects, uploaded my file to the YDNA Warehouse, my Haplogroup is R-BY186342 but I think they've got me as an upstream subclade R-A6526, my family we're from Ulster (Northern Ireland) Antrim. Nigel, do you have access to my file at YDNA Warehouse, if you don't, do I need to enable something, so you can? Nigel, just let me know what I need to do, to help you. Adh mor ort agus oiche mhaith.
Phil
When it comes to the Warehouse the Administration side of things are sparse. ?This will change over time as I build out tools to complement projects.
At the moment you have two files uploaded: ?sample_id | ? test? ? | filetype? -----------+-----------+---------- ?B654981 ? | Big Y-700 | vcf ?B654981 ? | Big Y-700 | bed
Either Garth needs to upload the STR CSV, or I can also use my roles as the YDNA-Warehouse Super User and a CTS4466+ Co-Admin to do it with your consent.
Thanks,
James
|
James, on you go, you've got my consent - I've joined all these projects to get results, share with others and build something for the future - if this helps you/us and the rest of CTS4466, I'm in.??
Slan
toggle quoted message
Show quoted text
Hi Nigel, Phil Millar (PJRM) here - FTDNA Kit No: B654981?-
an Admin, with my permission, when I was first joining projects, uploaded my file to the YDNA Warehouse, my Haplogroup is R-BY186342 but I think they've got me as an upstream subclade R-A6526, my family we're from Ulster (Northern Ireland) Antrim. Nigel, do
you have access to my file at YDNA Warehouse, if you don't, do I need to enable something, so you can? Nigel, just let me know what I need to do, to help you. Adh mor ort agus oiche mhaith.
Phil
When it comes to the Warehouse the Administration side of things are sparse. ?This will change over time as I build out tools to complement projects.
At the moment you have two files uploaded:
?sample_id | ? test? ? | filetype?
-----------+-----------+----------
?B654981 ? | Big Y-700 | vcf
?B654981 ? | Big Y-700 | bed
Either Garth needs to upload the STR CSV, or I can also use my roles as the YDNA-Warehouse Super User and a CTS4466+ Co-Admin to do it with your consent.
Thanks,
James
|
I recorded a quick 3 minute demonstration of how-to upload the STR CSV from FTDNA. ?It's pretty raw and the audio is janky, but it serves the purpose until I can go retrieve my audio recording gear from storage.
Hopefully this helps the more audio/visual learners.
Thanks,
James
|
add my stuff also,? ill try and get the bam file.? after the hundreds of dollars i've spent you would think this comes with it
|
i did this but the website doesnt generate any sort of message acknowledging anything.? hopefully it went in
|
Hi Marcia, are you from Sydney, NSW? Cheers. Matt
toggle quoted message
Show quoted text
On Saturday, July 16, 2022, Marcia McAvoy via <robertbuttles= [email protected]> wrote: Hi, ? I manage my deceased father’s DNA and had the Big Y DNA performed. His name is Richard McAvoy. I am not sure what results you have. I do not know what a BAM is and if you have my father's BAM. I have attached the his Big Y STR CSV.? Thanks, Marcia McAvoy On Jul 15, 2022, at 6:22 PM, James Kane <jkane@...> wrote:
? Hi folks,
Just a note for those who have participated in the past, the YDNA Warehouse is now importing Big Y STR CSVs beyond the 111 marker panels.? We will be using these to compute the ancestral values at each tree branch and adding them to the .? Currently, 8 of the 374 of you who have provided a BAM have also added the STR file with extended values.
CSV files are uploaded to a FTDNA STR or SNP Panel kit under your test Subject.
If the row above already exists click the Manage button, and follow the instructions at the bottom of the page.
And finally... the updates.? I have successfully realigned the 374 BAMs already in my possession to the telomere-to-telemore reference, CHM13 and HG002, being internally piloted by FTDNA's?G?ran Runstr?m.? These samples along with 1000 other fairly random ones are running through??to begin constructing a tree using this data.? As new potential branches are found under CTS4466, I'll share my findings here.
?also has access to the VCF and coverage BED files for this new accession.? Hopefully, you'll be able to see new updates show up there as well.
As always if you have trouble getting logged in or finding where to start send me a note directly by email.? We'll get you sorted out.
Thanks,
James Kane
PS: ?I plan to consolidate the STR, Big Y-500 and Big Y-700 tests into a single test unit in the future.? This will bring us more inline with how you all are used to a Big Y-700 being the test that gives you STRs these days at FTDNA.
|
Marcia, ? The BAM file is the BigY raw data file. Originally access to it came with the purchase of the BigY, but as only relatively few people requested the file and the provision of the file was not simple for FTDNA, FTDNA separated the BAM from their BigY product maybe 3 or 4 years ago. You do not have the Raw Data Product (BAM File) listed in your product history, so if you wanted it then you would have to purchase it from FTDNA. ? Regards Paul O’D ?
toggle quoted message
Show quoted text
From: [email protected] <[email protected]> On Behalf Of Matteo Sullivan
Sent: Tuesday, 6 September 2022 8:58 AM
To: [email protected]
Subject: Re: [R1b-CTS4466-Plus] YDNA Warehouse STR Uploads and Updates? Hi Marcia, are you from Sydney, NSW? Cheers. Matt
On Saturday, July 16, 2022, Marcia McAvoy via <robertbuttles=[email protected]> wrote: ? I manage my deceased father’s DNA and had the Big Y DNA performed. His name is Richard McAvoy. I am not sure what results you have. I do not know what a BAM is and if you have my father's BAM. I have attached the his Big Y STR CSV.?
On Jul 15, 2022, at 6:22 PM, James Kane <jkane@...> wrote:
? Hi folks,
Just a note for those who have participated in the past, the YDNA Warehouse is now importing Big Y STR CSVs beyond the 111 marker panels.? We will be using these to compute the ancestral values at each tree branch and adding them to the .? Currently, 8 of the 374 of you who have provided a BAM have also added the STR file with extended values.
CSV files are uploaded to a FTDNA STR or SNP Panel kit under your test Subject. 
If the row above already exists click the Manage button, and follow the instructions at the bottom of the page. 
And finally... the updates.? I have successfully realigned the 374 BAMs already in my possession to the telomere-to-telemore reference, CHM13 and HG002, being internally piloted by FTDNA's?G?ran Runstr?m.? These samples along with 1000 other fairly random ones are running through??to begin constructing a tree using this data.? As new potential branches are found under CTS4466, I'll share my findings here.
?also has access to the VCF and coverage BED files for this new accession.? Hopefully, you'll be able to see new updates show up there as well.
As always if you have trouble getting logged in or finding where to start send me a note directly by email.? We'll get you sorted out.
Thanks,
James Kane PS: ?I plan to consolidate the STR, Big Y-500 and Big Y-700 tests into a single test unit in the future.? This will bring us more inline with how you all are used to a Big Y-700 being the test that gives you STRs these days at FTDNA.
|
Phil Millar