gl2vcf error

[Alan Male]

Hi, I have been trying out the gl2vcf function on a genlight object.

However, I get this message:

31892 MB RAM detected; reserving 15946 MB for main workspace. Possibly irregular .ped line. Restarting scan, assuming multichar alleles. Rescanning .ped file... 43% Error: Half-missing call in .ped file at variant 54, line 650. How do I go about correcting it?

Best, 

AM

[Jose Luis Mijangos]

Hi Allan,

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