Error message by executing impute function

[laurasteinmann]

Hi,
I am trying to impute a whole-genome sequencing dataset with polyBreedR. I obtained a biallelic VCF and wanted to use this as input for the imputation. I run the function impute(input, output2, ploidy=2, method="RF", geno="GT", min.DP=1, max.missing=0.9, n.core = 40) and get the following Error Message:
Error in dim(newX) <- c(prod(d.call), d2) : the dims contain missing values Calls: impute -> apply In addition: Warning message: In dim(newX) <- c(prod(d.call), d2) : NAs introduced by coercion to integer range Execution halted
Can you tell me what other requirements the function needs to be able to execute it.
Best Laura

[jendelman]

Hello, based on the error message, it seems that maybe there is a formatting issue with your VCF file. I would suggest creating a small version of your dataset and see if it runs, while also visually inspecting the file with a text editor.