Population information
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RN Sarma
Jan 27, 2022, 5:32:18 AM1/27/22
to poppr
Can we put population information yo a genind file obtained from VCF format?
Zhian Kamvar
Jan 27, 2022, 10:18:59 AM1/27/22
to RN Sarma, poppr
Yes, this is possible. Javier Tabima and Brian Knaus wrote good tutorial on this: https://grunwaldlab.github.io/Population_Genetics_in_R/gbs_analysis.html
On Thu, Jan 27, 2022 at 2:32 AM 'RN Sarma' via poppr <po...@googlegroups.com> wrote:
Can we put population information yo a genind file obtained from VCF format?
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Brian Knaus
Jan 27, 2022, 12:19:37 PM1/27/22
to Zhian Kamvar, RN Sarma, poppr
My interpretation of the VCF specification
is that there is no 'concept' of population in VCF data. This means that there is no possible way to incorporate population data directly into the VCF data. This is why it needs to be added from some other source, as suggested in the link provided by Zhian.
HTH!
Brian
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Brian J. Knaus, Ph.D.
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