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  1. R1b-CTS4466-Plus
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Request for BAM Files for Realignment and Joint Genotyping

 

Sounds great, Alan.

Just to set a deadline for when I'll close this round of collection up... Any BAM submitted up until December 30th will be included. ?If it's received after expect to wait probably six months before I would be doing another call for new BAM files. ?Mostly to give time to try to work in the current FTDNA VCF only folks, and there are some other regions of my tree that need attention due to a lot more samples from the Human Genetic Diversity Project having been reprocessed from my pipelines.

James
 

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James

I have given you advanced access.

My kit B475646 is not listed in your BAM tracker spreadsheet.

Let me know if you need anything further.

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Matt

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From: R1b-CTS4466-Plus@groups.io <R1b-CTS4466-Plus@groups.io> On Behalf Of James Kane via groups.io
Sent: Wednesday, 4 December 2024 10:17 AM
To: R1b-CTS4466-Plus@groups.io
Subject: Re: [R1b-CTS4466-Plus] Request for BAM Files for Realignment and Joint Genotyping

?

Sounds great, Alan.

Just to set a deadline for when I'll close this round of collection up... Any BAM submitted up until December 30th will be included. ?If it's received after expect to wait probably six months before I would be doing another call for new BAM files. ?Mostly to give time to try to work in the current FTDNA VCF only folks, and there are some other regions of my tree that need attention due to a lot more samples from the Human Genetic Diversity Project having been reprocessed from my pipelines.

James
 

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I have granted James Kane advanced access to my kit, 169109.?

Dustin Shane?

On Dec 4, 2024, at 4:15?AM, Matt Ryan via groups.io <mattryan@...> wrote:

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James

I have given you advanced access.

My kit B475646 is not listed in your BAM tracker spreadsheet.

Let me know if you need anything further.

?

Matt

?

From: R1b-CTS4466-Plus@groups.io <R1b-CTS4466-Plus@groups.io> On Behalf Of James Kane via groups.io
Sent: Wednesday, 4 December 2024 10:17 AM
To: R1b-CTS4466-Plus@groups.io
Subject: Re: [R1b-CTS4466-Plus] Request for BAM Files for Realignment and Joint Genotyping

?

Sounds great, Alan.

Just to set a deadline for when I'll close this round of collection up... Any BAM submitted up until December 30th will be included. ?If it's received after expect to wait probably six months before I would be doing another call for new BAM files. ?Mostly to give time to try to work in the current FTDNA VCF only folks, and there are some other regions of my tree that need attention due to a lot more samples from the Human Genetic Diversity Project having been reprocessed from my pipelines.

James
 

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James, I've two files at the DNA Warehouse, Kit No.?B654981 & Kit No.?SI14537


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From: R1b-CTS4466-Plus@groups.io <R1b-CTS4466-Plus@groups.io> on behalf of James Kane via groups.io <jkane@...>
Sent: Wednesday, 4 December 2024 7:17 AM
To: R1b-CTS4466-Plus@groups.io <R1b-CTS4466-Plus@groups.io>
Subject: Re: [R1b-CTS4466-Plus] Request for BAM Files for Realignment and Joint Genotyping
?
Sounds great, Alan.

Just to set a deadline for when I'll close this round of collection up... Any BAM submitted up until December 30th will be included. ?If it's received after expect to wait probably six months before I would be doing another call for new BAM files. ?Mostly to give time to try to work in the current FTDNA VCF only folks, and there are some other regions of my tree that need attention due to a lot more samples from the Human Genetic Diversity Project having been reprocessed from my pipelines.

James
 

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On Dec 8, 2024, at 6:40?PM, Phil Millar via groups.io <pjr_millar@...> wrote:

James, I've two files at the DNA Warehouse,?Kit No.?B654981 &?Kit No.?SI14537

As long as your kits are in the Warehouse, you are good. ?That’s where I actually prefer to receive the files because it’s ultimately more secure and keeps you in the full ownership of your data. ?You’ll be seeing more about some tools I’m really close to releasing there soon.

This is mostly an effort to chase down folks who aren’t there and have raw data available.

Thanks,

James
 

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James, you already have clearance for Kit 165440.

Tom Mahoney

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From: R1b-CTS4466-Plus@groups.io <R1b-CTS4466-Plus@groups.io> on behalf of James Kane via groups.io <jkane@...>
Date: Friday, November 29, 2024 at 7:59?AM
To: R1b-CTS4466-Plus@groups.io <R1b-CTS4466-Plus@groups.io>
Subject: [R1b-CTS4466-Plus] Request for BAM Files for Realignment and Joint Genotyping

Hello folks,

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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.

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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:

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Option 1: Update Project Preferences

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Update your FTDNA account preferences to allow me, James Kane, Advanced access to your kit's profile. ?See this FTDNA knowledge article for how:

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Option 2: Create an Account on YDNA-Warehouse.org

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Alternatively, you can create an account on and add the Big Y test results. ?Several explanation videos are available here: ?

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What Happens to Your Data?

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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.

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If you have any questions or concerns about participating in this study, please don't hesitate to reach out. Thank you for your consideration!

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James Kane

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