dartR.base::gl2vcf

[Francisco José Franco Piccioli]

Hello, I need to transform Genlight data into a VCF (dartR.base::gl2vcf) for use with ShiNyP, but the following error occurs.

gl2vcf(x = data, outfile = "data_final.vcf")

system(..., intern = T)
3.
system_verbose(paste(plink.bin.path, "--file", prefix.in, "--recode",
"vcf", if (autosome.only) "--autosome "else "", "--allow-no-sex",
paste("--reference-allele", file.path(tempdir(), "mylist.txt")),
"--out", prefix.out, extra.options))
2.
make_plink(plink.bin.path = paste0(plink.bin.path, "/plink"),
extra.options = "--aec")
1.
gl2vcf(x = data, outfile = "data_final.vcf")

Best, regards,

Francisco

[Jose Luis Mijangos]

Hi Francisco,

I couldn't see any error message in the text you sent. 

Would you mind sending me a small subset of your data that replicates the behaviour you’re seeing to my email (luis.mijangos at gmail.com)? The code below shows how you can create and save a subset.

If you could please send me:

1. the file `test.rds` (from the code example below), and
2. the code you’re running,

that would be great.

library(dartRverse)

# subset loci
# you can increase the number of loci, for example n = 400
test <- gl.subsample.loci(your_data.gl, n = 200, method = "random")

# subset individuals
# you can adjust the number of individuals, e.g. indNames(test)[1:20]
test <- gl.keep.ind(test, ind.list = indNames(test)[1:10])

# save object in the working directory
saveRDS(test, "test.rds")

Cheers,
Luis

[Francisco José Franco Piccioli]

Hi Luis,

Thanks for your response. 

The error is as follows:

> gl2vcf(x = glsnp6,
+        outfile = "datos_FINAL_CONVERTIDOS.vcf")
Starting gl2vcf
  Processing genlight object with SNP data
  Chromosome information is not present in the slot 'chromosome'. Setting '0' as the name chromosome for all the SNPs.
Starting gl2plink
  Processing genlight object with SNP data
Completed: gl2plink

Error en system(..., intern = T): 'C:/proyectos_shiny/plink' not found



4.

system(..., intern = T)
3.
system_verbose(paste(plink.bin.path, "--file", prefix.in, "--recode",
"vcf", if (autosome.only) "--autosome" else "", "--allow-no-sex",
paste("--reference-allele", file.path(tempdir(), "mylist.txt")),
"--out", prefix.out, extra.options))
2.
make_plink(plink.bin.path = paste0(plink.bin.path, "/plink"),
extra.options = "--aec")
1.

gl2vcf(x = glsnp6, outfile = "datos_FINAL_CONVERTIDOS.vcf")

1.
gl2vcf(x = data, outfile = "data_final.vcf")  

Best regards, 

Francisco

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[Jose Luis Mijangos]

Hi Francisco,

As mentioned in the function documentation, you’ll need to download the binary file of PLINK 1.9 and provide its path in the plink.bin.path. By default, this points to the working directory, so the easiest option is just to place the binary file there.

You can download the binary here: https://www.cog-genomics.org/plink/

Let us know if we can help further.

Cheers,
Luis

[Bernd.Gruber]

gl.download.binary("plink", os = "windows", out.dir ="path" )

 

works as well to download the binary. (see variants below)

 

Cheers, Bernd

 

 

 

Arguments

software	name of the software package to download. Currently supported are: "epos", "NeEstimator", "Stairway2" and "Gone". Please note, depending on the software several files will be downloaded
os	the operating system to download the binary for. Currently supported are: "windows", "mac" and "linux". Please be aware some binaries are not available for all operating systems.
branch	which branch to download from (leave empty for the main branch and there should not be a reason to change that)
out.dir	the path where to save the binary. If left empty the binary will be saved in the temporary directory.

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[Francisco José Franco Piccioli]

Hi, Luis and Bernd.

Thank you very much for the information.

Best regards!

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