Last Call - Window Closes Dec 30th @ 12:59PM CST Re: Request for BAM Files for Realignment and Joint Genotyping
Please refer to the linked workbook. R1b-CTS4466+ BAM Tracker I have updated the tracker to consolidate some information on the FTDNA tab and added a "hs1 Complete?" column, which indicates that all Y DNA reads from any test have been merged into a single CRAM file, maximizing covered regions for joint genotyping. This file will be used to call the entire group in a single pass for every SNP found in any sample. The joint calling process is scheduled to begin on New Year's Eve morning. Thank you, James
Розпочато James Kane @
New R1b-CTS4466 View & Features at YDNA Warehouse
Merry Post-Christmas, I'm excited to announce a new view and features for the CTS4466 test data collected at YDNA-Warehouse with the launch of the Study system. For project members: Enhanced Data Visibility: Easily see which kits are in the warehouse and which test files have been uploaded. Access STR Chart data for Big Y Panels 6 and 7, currently unavailable from FTDNA. Download this data as a CSV file if desired. Utilize the internal mail system to contact close SNP matches tested outside of FTDNA. (Note: This feature requires the original warehouse submitter to have re-registered.) Customized Data Display: Control which data fields are displayed in the chart on the Studies tab: "Show Test Kits": Display your kit numbers at various labs (default: off). "Details": Show additional information about your most distant known paternal ancestor. "Show MDKA Origin": Display or hide the country of origin. "Show MDKA Birth Year": Display or hide the birth year. Note: Publicly turning on these options will make them visible to everyone on the Internet. The same experience as with FTDNA's projects. For project admins: Enhanced Project Management: Access the "Actions" drop-down menu: View SNPs: Generate a "Shared SNP" report for the participant. Move to Subgroup: Move participants to a different subgroup (note: everyone starts at their terminal SNP). Remove Member: Remove a member from the study. Contact Member: Use the internal mail system to contact them. View CRAM (disabled currently): View data in BAM submissions after realignment (coming soon). Investigator Settings: Update displayed fields on the Studies list. Update Membership Criteria: Access the Rules Engine to define study visibility. Add additional investigators to the Study (system admin only). Important Note: Participation in this site is entirely voluntary. If you're satisfied with FTDNA's Projects, please continue using their platform. This is an alternative that aims to address some of their perceived shortcomings. Thank you to all participants and those who have shared their data for this project. Sincerely, James Kane
Розпочато James Kane @
Question Re: [R1b-CTS4466-Plus] R1b-CTS4466+ BAM Tracker Re: Request for BAM Files for Realignment and Joint Genotyping 13
Free BAM? Hi James, I do not see my kit 539013 Frank Cashman on the excel file you provided. I have granted you advanced access. I'm not sure whether or not I'm due a free BAM. Let me know how I can help? Thanks, Barb Francis On Sat, Nov 30, 2024 at 8:20 AM James Kane via groups.io <jkane@...> wrote: I have created a Google Sheet to track this effort. You can check the status of a Big Y kit in the R1b-CTS4466+ Project, if you are due a free BAM from FTDNA, and if I have a copy analyzed already. The "Archive Prefix" column indicates I have retrieved a fresh BAM copy since 2024-11-26. The "BAM(s) Analyzed" are the tests I already have/had processed for this effort. https://docs.google.com/spreadsheets/d/1lSZjHby-vS5Qf4PGpWyd3xEmqPLw41W9Vg8utzHi7gY/edit?usp=sharing As always let me know if there are questions or concerns. Thanks, James
Розпочато barb francis @ · Останніх @
Deadline Approaching - Dec 30, 2024 Re: Request for BAM Files for Realignment and Joint Genotyping 10
There are ten days remaining on the collection round. Other than the last two received, everyone is I have is updated in the tracker sheet. https://docs.google.com/spreadsheets/d/1lSZjHby-vS5Qf4PGpWyd3xEmqPLw41W9Vg8utzHi7gY/edit?usp=sharing If you miss the bus, it will be summer 2025 before there is another opportunity at the soonest. Thanks to everyone who has responded so far. James Kane
Розпочато James Kane @ · Останніх @
R1b-CTS4466+ BAM Tracker Re: Request for BAM Files for Realignment and Joint Genotyping 13
I have created a Google Sheet to track this effort. You can check the status of a Big Y kit in the R1b-CTS4466+ Project, if you are due a free BAM from FTDNA, and if I have a copy analyzed already. The "Archive Prefix" column indicates I have retrieved a fresh BAM copy since 2024-11-26. The "BAM(s) Analyzed" are the tests I already have/had processed for this effort. https://docs.google.com/spreadsheets/d/1lSZjHby-vS5Qf4PGpWyd3xEmqPLw41W9Vg8utzHi7gY/edit?usp=sharing As always let me know if there are questions or concerns. Thanks, James
Розпочато James Kane @ · Останніх @
Request for BAM Files for Realignment and Joint Genotyping 26
Hello folks, I am preparing a new set of joint call files for the R1b-CTS4466 subclade and its parent R1b-FGC11134 subclade. To achieve this, I need to collect BAM files from individuals who have taken the Big Y test. If you have granted me Advanced access via GAP (Group Access Program), you already have a BAM file available for use. However, if you have not done so and have purchased your Big Y BAM test results, please take the following steps: **NOTE** Do not construe this as a request to make a purchase for something you don't already own. The BAMs are a nice to have for your own data portability not a necessity. Option 1: Update Project Preferences Update your FTDNA account preferences to allow me, James Kane, Advanced access to your kit's profile. See this FTDNA knowledge article for how: https://help.familytreedna.com/hc/en-us/articles/4401855065743-Setting-Project-Preferences#group-project-administrator-access-0-0 Option 2: Create an Account on YDNA-Warehouse.org Alternatively, you can create an account on YDNA-Warehouse.org and add the Big Y test results. Several explanation videos are available here: https://ydna-warehouse.org/submit.php What Happens to Your Data? Once I have received your BAM file, it will be realigned using BWA MEM and used to generate new SNP and INDEL calls. The data will also contribute to an update of the maximum likelihood tree with branch age estimates published with a Creative Commons license. If you have any questions or concerns about participating in this study, please don't hesitate to reach out. Thank you for your consideration! James Kane EDITED FOR CLARIFICATION
Розпочато James Kane @ · Останніх @
FtDNA Project
Hi James, Thank you for this massive project you are doing! I manage Kit 977130. Advanced perms were given to you. I also did not have the option to download the BAM file, but I did upload the VCF Big Y on ydna warehouse. Hope this helps!
Розпочато Crystal McCartney @
Account access and BAM files
James, I manage three files at FTDNA, Philip Millar: Kit No. B654981 , James Millar: Kit No. SI14537 and Jonathan Millar: Kit No. SI15654, access to those accounts have been set to 'Advanced', also, James and I are at the DNA Warehouse - I haven't got round to uploading Jono's file yet - do you have access to our info or do I need to do something else to help you? James, we're all A212s, I don't know if that is within the parameters of your current endeavor, if our info is, I hope it helps you. James, if I need to do anything else, for you to access our files, then just let me know. Slan go foill Phil
Розпочато Phil Millar @
Success stories 5
Hello cousins! Does anyone in the group have success stories to share, whether in the y line or aDNA? It might inspire some upgrades that could help the group :). For me, and I am American for context, my father's family always identified as Irish Catholic but with a surname that seemed at odds (Adams). Indepedent of DNA testing, via research and family lore, I found cousins in Armagh who said we were Quakers who converted to Catholicism in the late 18th century. Via DNA, I found a Scottish origin between the 1100s and 1200s, centered around Renfrewshire. Via this group's research, I suspect an early medieval Irish Gaelic origin, possibly from the Cianachta. On other lines, I sorted between two 18th century Campbell lines in colonial Virginia, found an ancestral "Indian princess" US line and found my wife's unexpected Jamaican African roots. Anyone else have useful revelations to share?
Розпочато Michael Adams @ · Останніх @
Y500 With Zero People with Father's or Mother's Maiden Last Name 15
I have reached our by FTDNA by email asking them if perhaps some error was made with my Big Y 700 test because there is not one person in the results who is in my family history, nor anyone with my father's last name, nor my mother's birth name. I've received no response except for an acknowledgement of my request. Is it unusual to have zero results with my last name? Regards, David J. Ring, Jr. Great Grandson of David A. Ring of Cork, Ireland.
Розпочато D.J.J. Ring, Jr. @ · Останніх @
Changes to YDNA Warehouse R-CTS4466 Tree 5
Hi folks, I’ve rewritten most of the tree viewer for YDNA Warehouse to make it load faster and include more information. It can actually render FTDNA’s full tree from A to the leaves in 5 seconds without the kits on my test machine… unfortunately they don’t allow for reuse of their information for non-private use though. In the extract of R-A804 below, you can see the sample donor box has been reworked to separate the MDKA’s surname and year of birth when provided. The type of test with the most coverage available is noted in the upper right hand corner. If the sample has a blue background instead of gold, it’s a VCF/BED submission instead of BAM file. It’s the samples with the gold backgrounds that are the basis of the TMRCA calculations. Red background samples are Ancient DNA but not all of those have been marked correctly yet. Finally, the indigo background samples are for folks from 23&Me, AncestryDNA, etc... The circled box which is referred to as the Taxa ID will become customizable in the near future. You will be able to select your FTDNA/FGC/YSEQ/etc kit for this purpose. I’m also considering allowing it to be used for other indicators like holders of verified royal titles. That would be a more manual process for verification purposes however. The long standing “bug” when you hit enter after typing in the Search by Branch or SNP has been addressed and works to reload the tree based one the search instead of needing to use the Tab key. Phylogenetic Tree ydna-warehouse.org As always if you would like to be included in this tree, your raw data needs to be uploaded. Should you need assistance reach out. Thanks, James Kane
Розпочато James Kane @ · Останніх @
Y700 With Zero People with Father's or Mother's Maiden Last Name 2
I knew from family notes that my male ancestors were Ryan. I was told it was originally O'Ryan and anglicized to Ryan and from there to Ring. I always loved Munster cheese. So now I know why. I have not found any explanations of the results pages of the Y700 results, so I'm poking around and looking without any guide. Regards, DR Regards, David
Розпочато D.J.J. Ring, Jr. @ · Останніх @
CTS4466 Question 6
I'm adopted. I've discovered my birth mother, but she's passed and I can't narrow down my father. Thru Ancestry I can narrow down relatives, but i'm 99% sure most are from my father's mother. Through 23andMe I've found out my that haplogroup is CTS4466 and only two men that I'm related to share that with me and share 3rd great grandparents. Both are named Gilliam. My observations tell me that my "terminal" haplogroup might not actually be CTS4466. Does this sound correct? Thank you, Rick Smith
Розпочато rickwsmith@... @ · Останніх @
My Irish Type II tree 17
Thank you Lucas for intervening, I fully agree with your remarks. But David, I am not sure how you have derived the ‘From McCarthy tree’ allele values. If you track the STRs all the way from the block just below L21 at the top of sheet 2 down to FT43021 on sheet 11 – which I admit takes a bit of work! – you should find that by the time you reach 576: 18>19 (at the time of FT43021 itself), none of the others has changed. The tree construction is not automated in this respect so I will be more than happy to hear of apparent errors – I am sure there will be occasional ones - but they should be thoroughly checked out first. I do not have time to deal with a large number of what turn out to be spurious queries. I do though appreciate participants ensuring the validity of what they see, and letting me know about apparent errors*. They should first ensure they understand the Legend shown on Sheet 1. Combining STR analysis with the SNP data similar to that shown in FTDNA’s haplotree and its Block Tree views thereof, does result in a presentation packed with detail, but, as my ‘legacy’, since co-founding the project with Elizabeth ten years ago, I still believe it is best all presented in one place. * But first wait for the new update targeted for the end of this month! Kind regards = Nigel McCarthy Sent from Mail for Windows
Розпочато Nigel McCarthy @ · Останніх @
R-A7752 Moynihan and Mooney 8
We now have a Mooney sharing the same branch as Moynihan. The hope for this to happen was discussed in our post from October. Nigel, or anyone else, does the addition of Mr. Mooney give any further insight into this area of the Big Y Tree? Sue Minnehan
Розпочато Francis & Susan Minnehan @ · Останніх @
Ok
Розпочато Tom O'Hanlon @
Question for Nigel 3
Hi Nigel, regarding my previous question about Fran’s new Moynihan Y-700 match and your comments, is it ok if I screenshot your comments and share them with the wife of Mr. Moynihan who I’m communicating with? Also would it be ok if I shared page 24 of your tree which shows where these branches are located, as well as page 1 with your note #26. I’m also thinking of sending this information to Fran’s two Mooney Y-111 matches as maybe it would make them consider upgrading to Y-700. Would that be ok? I appreciate all your assistance. Best regards, Sue Minnehan
Розпочато Francis & Susan Minnehan @ · Останніх @
New Match on Big Y 18
Greetings all, in my never ending pursuit to try to figure out my husband’s Minihan/Moynihan ancestors, any comments and explanations about the following information will be greatly appreciated. in July a new Y-111 match with the surname of Moynihan posted with a genetic distance of 10 steps. Very soon thereafter an upgrade to Big Y was done. The results have posted and Mr. Moynihan has been assigned to haplogroup R-A7752. What is that telling us, if anything? Or just that his ancestors and my husband’s ancestors are so far back that it’s impossible to find the connection? Here’s a screenshot. Can anyone tell me what this means? Thanks all! Sue & Fran Minnehan
Розпочато Francis & Susan Minnehan @ · Останніх @
Irishorigenes etc 2
Hi Espen, Yes, I know of Dr Tyrone Bowes and his various Origenes websites (IrishOrigenes, ScottishOrigenes and EnglishOrigenes). I met Dr Bowes at the 2nd Genetic Genealogy Ireland Conference in Dublin in October 2014 where he described his methodology. I followed up with him during the following year about aspects of this. Whilst genetic genealogy has exploded over the past 10 years, Dr Bowes methodology was then (and to a large extent is still) based on the longstanding associations between surnames and geographical locations. Even back in 2015 I was arguing with him that this was not applicable in all instances - ' I have to disagree to a certain extent with you about surnames and locations. I agree that some names, and some branches of other names, can and do have long-term associations with a given location but others have clearly been subjected to dispersal pressures after surnames were adopted (the Great Famine being a recent example of a series of similar crises). And, no doubt, some people would have been subject to similar pressures before the adoption of surnames if they were unlucky enough to have been in the wrong place at the wrong time? And now traceable through SNP's?'. I now realise that many of these dispersal pressures also occurred before the adoption of hereditary surnames. In the case of the A151+ sub-branches of of CTS4466 / A541, I think that that Dr Bowes' methodology may lead to misleading results given that much of the further branching of this line occurred before the adoption of hereditary surnames in Ireland, Britain or Scandinavia and also given the wide geographical spread of this haplotype across Ireland, Britain and Scandinavia over a thousand years ago This is further compounded by the relatively small numbers of men identified thus far in these sub-branches. Dr Bowes certainly produces very visually striking case reports as illustrated in the case studies on his web sites but I would be doubtful that you would learn much more from him than from this group and your Big Y.. We would definitely learn more if we could identify and test more men who are A151+! All the best, John Brazil. On Tue, Aug 8, 2023 at 5:43 PM Espen Solheim <espheim@...> wrote: Hi Hope all is well! Have a question regarding Irish origenes (https://www.irishorigenes.com/content/re-writing-history). Anyone have any experience with the consultation and what can I as a Norwegian potentially learn that isn’t already known through this group and the DNA results from the big y itself? Espen Solheim/Johnsen
Розпочато john brazil @ · Останніх @
What ChatGPT Thinks of CTS4466 4
Hi Hope all is well! Have a question regarding Irish origenes (https://www.irishorigenes.com/content/re-writing-history). Anyone have any experience with the consultation and what can I as a Norwegian potentially learn that isn’t already known through this group and the DNA results from the big y itself? Espen Solheim/Johnsen
Розпочато Espen Solheim @ · Останніх @
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