PopGenome - readData error

Question

[conny.sjoqvist]

Hi!

Have anyone experienced this type of error in PopGenome when reading in the VCF-file?

> BACL30_104 <- readData ("104_vcf", format="VCFhap", gffpath="104_gff")
|            :            |            :            | 100 %
|(!!)   Translation failed in file 104_vcf/BACL30_104_full.vcf!
Error in CCC$matrix : $ operator is invalid for atomic vectors

For simplicity, I have a vcf-file of only one sample in the "104_vcf" folder. The file was produced by Freebayes.

[RedPanda]

Hi,

i have the same issue. Did you have found any solution for this?

Best regards

Answer 1

[Ace]

I know this post is past its prime, but I recently had this same error and thought I'd help out anyone else that happened to come across this post looking for answers. I found that it is resolved by using their "split_into_scaffolds" function, rather than manually splitting as some people have recommended.

https://rdrr.io/cran/PopGenome/man/VCF_split_into_scaffolds.html