File issues

[HanYanggggggg]

hello cbirdlab，
I have a question, I hope you can answer it when you see it.
How to write this file? /home/cbird/Projects/PuntioplitesFalcifer/mkBAM2/popmap.3.7
Thank you and looking forward to your reply.

[cbird808]

Short answer, ddocent (puritz) or ddocent hpc (bird). Possibly freebayes, but I'd have to look at the code. Get Outlook for Android<https://aka.ms/AAb9ysg>

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________________________________ From: HanYanggggggg ***@***.***> Sent: Tuesday, April 23, 2024 2:10:39 AM To: cbirdlab/pgdspider_scripts ***@***.***> Cc: Subscribed ***@***.***> Subject: [cbirdlab/pgdspider_scripts] File issues (Issue #1) hello cbirdlab， I have a question, I hope you can answer it when you see it. How to write this file? /home/cbird/Projects/PuntioplitesFalcifer/mkBAM2/popmap.3.7 Thank you and looking forward to your reply. — Reply to this email directly, view it on GitHub<#1>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ADBV4SZEPIIELMN2N4WVADTY6YCO7AVCNFSM6AAAAABGUH2QOWVHI2DSMVQWIX3LMV43ASLTON2WKOZSGI2TQMJSHA3TCNY>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[cbird808]

Additionally, it's a simple tsv file that you could make by hand. In the context of pgd spider, it's associating group affiliation with library ID. Get Outlook for Android<https://aka.ms/AAb9ysg>

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________________________________ From: Bird, Chris ***@***.***> Sent: Tuesday, April 23, 2024 10:15:47 AM To: cbirdlab/pgdspider_scripts ***@***.***>; cbirdlab/pgdspider_scripts ***@***.***> Cc: Subscribed ***@***.***> Subject: Re: [cbirdlab/pgdspider_scripts] File issues (Issue #1) Short answer, ddocent (puritz) or ddocent hpc (bird). Possibly freebayes, but I'd have to look at the code. Get Outlook for Android<https://aka.ms/AAb9ysg>

________________________________ From: HanYanggggggg ***@***.***> Sent: Tuesday, April 23, 2024 2:10:39 AM To: cbirdlab/pgdspider_scripts ***@***.***> Cc: Subscribed ***@***.***> Subject: [cbirdlab/pgdspider_scripts] File issues (Issue #1) hello cbirdlab， I have a question, I hope you can answer it when you see it. How to write this file? /home/cbird/Projects/PuntioplitesFalcifer/mkBAM2/popmap.3.7 Thank you and looking forward to your reply. — Reply to this email directly, view it on GitHub<#1>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ADBV4SZEPIIELMN2N4WVADTY6YCO7AVCNFSM6AAAAABGUH2QOWVHI2DSMVQWIX3LMV43ASLTON2WKOZSGI2TQMJSHA3TCNY>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[HanYanggggggg]

@cbird808
Thank you for your answer.
And I found a post about this file that was very helpful to me, and I also hope that people with similar issues can see it.
https://www.biostars.org/p/18330/

[cbird808]

Pgd spider will convert your vcf to another format. All of the data in the VCF will be used From: Yaaaaaang ***@***.***> Sent: Tuesday, April 23, 2024 7:20 PM To: cbirdlab/pgdspider_scripts ***@***.***> Cc: Bird, Chris ***@***.***>; Mention ***@***.***> Subject: Re: [cbirdlab/pgdspider_scripts] File issues (Issue #1) @cbird808<https://github.com/cbird808> Another question, does my input VCF file need to include only one individual from each of my groups? In my experiment, there were 26 individuals, is that correct? - Reply to this email directly, view it on GitHub<#1 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ADBV4SY2VNUMJ5PPSMJWJVDY633ENAVCNFSM6AAAAABGUH2QOWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANZTGY4TQMJQGI>. You are receiving this because you were mentioned.Message ID: ***@***.******@***.***>>