Polyploidy found, and not supported by vcftools for a diploid data set.

Question

[Shripathi]

Hi, I used gatk mutect2-select variant (retained only SNPs)-combinegvcfs to generate a vcf file for a diploid species. When I tried to process the vcf file using vcf tools, some of the commands did work, however, when it comes to individual missingness, I get "Polyploidy found, and not supported by vcftools" error. does anyone have the same experience? I ran SNP calling modules using standard commands suggested in gatk Best practices.

regards, Shri

[Pierre Lindenbaum]

vcftools is deprecated. use bcftools.

[Shripathi]

Thank you Pierre.