PolyRAD VCF2RADdata Error - "Either possiblePloidies or taxaPloidy must consist entirely of even numbers" - Is this a bug?

[YI-164]

Dear PolyRAD developers/community, I am encountering an error when using the VCF2RADdata function in PolyRAD and would like to confirm whether this is expected behavior or a potential bug.

Error message:
Either possiblePloidies or taxaPloidy must consist entirely of even numbers.

My setup:

Sample ploidy: Taro (Colocasia esculenta) - mixture of diploid samples and triploid samples Variant calling: FreeBayes with triploid settings Sample information: CSV file containing ploidy levels for each sample

Code used:

rsample_info <- read.csv("ploidy.csv", stringsAsFactors = FALSE)

# Create taxaPloidy vector
ploidy_vector <- sample_info$Ploidy
names(ploidy_vector) <- sample_info$SampleName

# Extract possible ploidies
mydata <- VCF2RADdata(
  file = "satoimo_filtered.vcf",
  possiblePloidies = list(2,3),
  taxaPloidy = ploidy_vector,
  min.ind.with.reads = 50,
  min.ind.with.minor.allele = 2,
  expectedAlleles = 500000,
  yieldSize = 500000,
  refgenome = "Taro_Lachesis_assembly_Chr.fa"
)

Question: Is this error expected behavior when working with triploid organisms? The error suggests that PolyRAD requires even ploidy numbers, but taro is naturally triploid (3n). Should I:

Modify my approach to work with triploid data in PolyRAD? Use different parameters or preprocessing steps? Is this a limitation of the current PolyRAD version for odd-ploidy organisms?

Any guidance on handling triploid organisms in PolyRAD would be greatly appreciated. Thank you for your time and assistance.

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