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.

---

I am not good at English, so I used Claude to make this message.

[lvclark]

Assuming that ploidy_vector contains the integers 2 and 3, just set possiblePloidies to 2. TaxaPloidy pertains to samples, and possiblePloidies pertains to loci. They are multiplied together and divided by 2 to get the final ploidy.

…

On Mon, Aug 4, 2025, 12:46 AM YI-164 ***@***.***> wrote: *YI-164* created an issue (lvclark/polyRAD#45) <#45> 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. — Reply to this email directly, view it on GitHub <#45>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADG72KH5XCBW7SPPKJG6RZL3L3QS7AVCNFSM6AAAAACDA5LQKKVHI2DSMVQWIX3LMV43ASLTON2WKOZTGI4DOOJZG4YDANQ> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[YI-164]

Thank you for the quick response.
I was able to understand that part and parse it successfully!
Thank you so much!