Does R/qtl works best for polyploid species like peanut (allotetraploid)

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Naveen Kumar

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Jul 5, 2022, 12:10:47 AM7/5/22
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Hello all,

I have a VCF file from a RIL population of around 300 lines and when I tried this code to convert VCF to R/qtl format:

vcf <- readVcf(" vcffile")
snp.matrix <- genotypeToSnpMatrix(vcf, uncertain = FALSE)
snp.matrix.transposed <- t(as(snp.matrix$genotypes, "character"))
write.table(snp.matrix.transposed, "SNP_matrix_test.csv", sep="\t")


The snp.matrix file generated from this shows all NA and the warning is " non-diploid variants are set to NA". what is the way forward? 

Thanks.



Karl Broman

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Jul 5, 2022, 2:44:16 PM7/5/22
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The genotypeToSnpMatrix function is part of the variantAnnotation package, so maybe talk to the authors of that package.

karl

On Jul 4, 2022, at 11:10 PM, Naveen Kumar wrote:

Hello all,
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Naveen Kumar

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Jul 5, 2022, 2:49:33 PM7/5/22
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Dear Karl,

Thanks for the reply. 

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