Request for BAM Files for Realignment and Joint Genotyping

James Kane All Messages By This Member #857 Edited 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: ? Option 2: Create an Account on YDNA-Warehouse.org ? Alternatively, you can create an account on and add the Big Y test results. ?Several explanation videos are available here: ? ? 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
Ed Aber Leek All Messages By This Member #858 364427 done toggle quoted message Show quoted text On Fri, Nov 29, 2024 at 9:05?AM James Kane via <jkane=[email protected]> wrote: [Edited Message Follows] 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: ? Option 2: Create an Account on YDNA-Warehouse.org ? Alternatively, you can create an account on and add the Big Y test results.? Several explanation videos are available here: ? ? 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
Peter Edwards All Messages By This Member #859 开云体育 Peter Edwards: 169169. Done. If problem accessing let me know.? Peter toggle quoted message Show quoted text On Nov 29, 2024, at 10:05, James Kane via groups.io <jkane@...> wrote: ? [Edited Message Follows] 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: ? Option 2: Create an Account on YDNA-Warehouse.org ? Alternatively, you can create an account on and add the Big Y test results. ?Several explanation videos are available here: ? ? 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
David Delacy All Messages By This Member #860 Am i already on the list?
James Kane All Messages By This Member #861 On Nov 29, 2024, at 3:17?PM, David Delacy via groups.io <beerandcandy2010@...> wrote: Am i already on the list? Hi David, I’m showing your kit# as having received the BAM in the YDNA Warehouse. You’re just waiting while I round up some more stragglers. Mostly men who are on branches I think may have some analysis problems in FTDNA’s tree. Those who have accounts there can quickly check if I have a BAM with the test traffic lights from the samples Management button. If the tests are green, I have the BAM. If the tests are light blue, I only have the VCF report provided by FTDNA. These can't be realigned when new references are made available. Thanks, James PastedGraphic-1.png PastedGraphic-2.png
Jack O'Keefe All Messages By This Member #862 开云体育 Hi James, ? I’ve granted advanced access to you for both #1166433 (John O’Keefe) and #439092 (Nathan O’Keefe). John is BigY500 and Nathan BigY700. ? Cheers, Jack O’Keefe ? toggle quoted message Show quoted text From: [email protected] <[email protected]> On Behalf Of James Kane via groups.io Sent: Friday, November 29, 2024 8:06 AM To: [email protected] Subject: [R1b-CTS4466-Plus] Request for BAM Files for Realignment and Joint Genotyping ? [Edited Message Follows] 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: ? Option 2: Create an Account on YDNA-Warehouse.org ? Alternatively, you can create an account on and add the Big Y test results. ?Several explanation videos are available here: ? ? 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
James Kane All Messages By This Member #863 开云体育 On Nov 29, 2024, at 12:44?PM, Jack O'Keefe via groups.io <jack53705@...> wrote: I’ve granted advanced access to you for both #1166433 (John O’Keefe) and #439092 (Nathan O’Keefe). John is BigY500 and Nathan BigY700. Thank you. ? I have John’s Big Y BAM. ?Nathan is tested on Big Y 700 and FTDNA doesn’t provide free BAMs without those they were originally tested on Big Y 500. ?I grabbed his VCF though since I didn’t have a copy. Just to be clear Big Y 700 testers should not purchase the BAM unless you want it for your own records. ?The $100 would be better spent on down payments on testing more relatives. James
Daniel Erwin All Messages By This Member #864 Dear James, ? ? ? You should?now have access to my file via FTDNA account?preferences. ? ? ??Thank?you for the head's?up and happy holidays to all. Tim Erwin toggle quoted message Show quoted text On Fri, Nov 29, 2024 at 2:19?PM James Kane via <jkane=[email protected]> wrote: On Nov 29, 2024, at 12:44?PM, Jack O'Keefe via <jack53705=[email protected]> wrote: I’ve granted advanced access to you for both #1166433 (John O’Keefe) and #439092 (Nathan O’Keefe). John is BigY500 and Nathan BigY700. Thank you. ? I have John’s Big Y BAM.? Nathan is tested on Big Y 700 and FTDNA doesn’t provide free BAMs without those they were originally tested on Big Y 500.? I grabbed his VCF though since I didn’t have a copy. Just to be clear Big Y 700 testers should not purchase the BAM unless you want it for your own records.? The $100 would be better spent on down payments on testing more relatives. James
Debbie Starr All Messages By This Member #865 开云体育 Have I given permission?? Debbie Starr (David Lundergan) Sent from my itty bitty iPhone keyboard toggle quoted message Show quoted text On Nov 29, 2024, at 4:48?PM, Daniel Erwin via groups.io <timothy.erwin@...> wrote: ? Dear James, ? ? ? You should?now have access to my file via FTDNA account?preferences. ? ? ??Thank?you for the head's?up and happy holidays to all. Tim Erwin On Fri, Nov 29, 2024 at 2:19?PM James Kane via <jkane=[email protected]> wrote: On Nov 29, 2024, at 12:44?PM, Jack O'Keefe via <jack53705=[email protected]> wrote: I’ve granted advanced access to you for both #1166433 (John O’Keefe) and #439092 (Nathan O’Keefe). John is BigY500 and Nathan BigY700. Thank you. ? I have John’s Big Y BAM.? Nathan is tested on Big Y 700 and FTDNA doesn’t provide free BAMs without those they were originally tested on Big Y 500.? I grabbed his VCF though since I didn’t have a copy. Just to be clear Big Y 700 testers should not purchase the BAM unless you want it for your own records.? The $100 would be better spent on down payments on testing more relatives. James
Dennis Murphy All Messages By This Member #866 开云体育 I have granted you advanced access.? Is that all I need to do? ? Dennis ? toggle quoted message Show quoted text From: [email protected] <[email protected]> On Behalf Of James Kane via groups.io Sent: Friday, November 29, 2024 5:56 AM To: [email protected] Subject: [R1b-CTS4466-Plus] Request for BAM Files for Realignment and Joint Genotyping ? 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 still have your Big Y?test results, please take the following steps: ? 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: ? Option 2: Create an Account on YDNA-Warehouse.org ? Alternatively, you can create an account on and add the Big Y test results. ?Several explanation videos are available here: ? ? 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
James Kane All Messages By This Member #867 开云体育 On Nov 29, 2024, at 4:27?PM, Dennis Murphy via groups.io <dmmurphy1@...> wrote: I have granted you advanced access.? Is that all I need to do? Yes, Advanced access allows to me to operator as your proxy to gather the files needed for this. ?I had your original but it looks like you’ve upgraded to 700 which will fill in gaps after I merge the two files. Thanks, James
Heather McKinley All Messages By This Member #871 James, I have updated preferences to allow you advanced access to kit IN133317. I hope this is?helpful. Best regards, Heather toggle quoted message Show quoted text On Fri, 29 Nov 2024, 13:55 James Kane via , <jkane=[email protected]> wrote: 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 still have your Big Y?test results, please take the following steps: ? 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: ? Option 2: Create an Account on YDNA-Warehouse.org ? Alternatively, you can create an account on and add the Big Y test results.? Several explanation videos are available here: ? ? 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
Michael Lee All Messages By This Member #872 开云体育 James, I just confirmed that you have advanced access. Incidentally, we have confirmed that the ancestors of our “Lee” family were actually “Leahy.” (It certainly explains a lot!) We have additional professional research underway. Michael Lee toggle quoted message Show quoted text On Nov 29, 2024, at 3:51?PM, James Kane via groups.io <jkane@...> wrote: ?On Nov 29, 2024, at 3:17?PM, David Delacy via groups.io <beerandcandy2010@...> wrote: Am i already on the list? Hi David, I’m showing your kit# as having received the BAM in the YDNA Warehouse. You’re just waiting while I round up some more stragglers. Mostly men who are on branches I think may have some analysis problems in FTDNA’s tree. Those who have accounts there can quickly check if I have a BAM with the test traffic lights from the samples Management button. If the tests are green, I have the BAM. If the tests are light blue, I only have the VCF report provided by FTDNA. These can't be realigned when new references are made available. Thanks, James <PastedGraphic-1.png> <PastedGraphic-2.png>
SallyH All Messages By This Member #874 Hi James, ? My husband's BigY-700 is in the warehouse, kit #B94719. ? You now have advanced access to his info in the FTDNA project. ? Sally ?
Debbie Starr All Messages By This Member #875 开云体育 Hi James, Do I need to request the BAM?? Warm regards, Debbie Starr (David Lundergan) Sent from my itty bitty iPhone keyboard toggle quoted message Show quoted text On Nov 30, 2024, at 5:34?PM, SallyH via groups.io <hoosierancestorsdna@...> wrote: ? Hi James, ? My husband's BigY-700 is in the warehouse, kit #B94719. ? You now have advanced access to his info in the FTDNA project. ? Sally ?
James Kane All Messages By This Member #876 开云体育 On Nov 30, 2024, at 5:42?PM, Debbie Starr via groups.io <constellations@...> wrote: Hi James, Do I need to request the BAM?? Warm regards, Debbie Starr (David Lundergan) Sent from my itty bitty iPhone keyboard Nope. ?Your husband’s files are prepped and waiting everyone else right now.

James