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Tools to handle tetraploid vcf

Hello,

I have a .vcf file produced with GATK, containing SNP variants of 32 samples of tetraploid Triticum species, so basically the GT field in the vcf has 4 values. I would like to use it in order to perform some nucleotide diversity analysis but softwares as vcftools and plink do not support polyploidy.

Do you have any suggestion on suitable softwares or how to "convert" the vcf in order to make it usable?

Many thanks,

Alice

vcf polyploid
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updated by Ram Ram • written by Alice • Alice

please define

some nucleotide diversity analysis

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written by Pierre Lindenbaum Pierre Lindenbaum

Thanks for answering. Mainly Fst, Nucleotide diversity (pi), Watterson's Theta

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written by Alice • Alice

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