Re: [dartR] Genlight to VCF

[Jose Luis Mijangos]

Hi Dallas,

You can try with the dartR function gl2vcf(). To be sure that everything works fine, you can install the developing version of dartR before using this converting function with:

library(dartR)

dartR::gl.install.vanilla.dartR(flavour="dev”)

And then restart your Rstudio session.

I am also attaching a tutorial to guide you through the process of reading your data into dartR.

Cheers,

Luis 

[Dallas]

Hey Jose,

Thanks for your help. I was wondering if you could help with another issue I have coming up? I'm trying to just create my genlight object, which I've done many times in the past, but now I'm getting this error:

Error in utils.read.dart(filename = filename, nas = nas, topskip = topskip, :
object 'tdummy' not found

I haven't been able to figure out how to fix it. I'm confused because I'm not calling on any objects in my script. This is the line of code I'm trying to run:

gl <- gl.read.dart(filename = "coanalyzed_imputed_1_row.csv", ind.metafile = "coanalyzed_ind_metrics.csv", topskip = 6, probar = TRUE)

Thank you for your help!

Dallas

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On 14 Jan 2022, at 8:54 am, Dallas <dallasan...@gmail.com> wrote:

Does anyone have experience converting a genlight object to a vcf file? I've been trying to use genomic_converter(), but have not been successful.

Thanks,

Dallas

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[Jose Luis Mijangos]

Hi Dallas,

Can you try using the function without specifying the parameter "topskip":

gl <- gl.read.dart(filename = "coanalyzed_imputed_1_row.csv", ind.metafile = "coanalyzed_ind_metrics.csv", topskip = 6, probar = TRUE)

Cheers,

Luis

[Dallas]

That worked - thank you!

Dallas

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[Dallas]

Hi Jose,

Sorry running into another issue today. Again I'm trying to create my genlight object in the dev version of dartR, and I keep getting an error saying that the function gl.read.dart could not be found. Do you know how I might solve this?

Again your help is much appreciated!

Dallas

[Dallas]

Haha, oh no as soon as I sent that and after all my searching I finally realized I just forgot to load the package to library after installing it... Please ignore my message!

Dallas