Tools to handle tetraploid vcf

Question

[Alice]

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

[Pierre Lindenbaum]

please define

some nucleotide diversity analysis

[Alice]

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