This might not be an software issue, but would it be okay if I could ask for theoretical question regarding running Dsuite?
I want to run Dsuite for taxa that are polyploid consisting diploid and triploid. Since, Dsuite can only work on bi-allelic sites, I have removed all the tri-allelic sites and convert triploid alleles to have only diploid by converting their heterozygous genotype from 0/1/1 or 0/0/1 to 0/1 in VCF. However ABBA BABA relies on allele frequencies which normally should be 50:50 if the sample is diploid. Hence would it be okay if I divide the 2 copy allele's frequency by half in triploid in the AD field? Would their be any vacillation in terms of theory?
Sorry I realized that allele frequency is not the AD in VCF file but rather allele frequency in population.
Kind regards,
Shane
Hi,
This might not be an software issue, but would it be okay if I could ask for theoretical question regarding running Dsuite?
I want to run Dsuite for taxa that are polyploid consisting diploid and triploid. Since, Dsuite can only work on bi-allelic sites, I have removed all the tri-allelic sites and convert triploid alleles to have only diploid by converting their heterozygous genotype from 0/1/1 or 0/0/1 to 0/1 in VCF. However ABBA BABA relies on allele frequencies which normally should be 50:50 if the sample is diploid. Hence would it be okay if I divide the 2 copy allele's frequency by half in triploid in the AD field? Would their be any vacillation in terms of theory?
Sorry I realized that allele frequency is not the AD in VCF file but rather allele frequency in population. Kind regards, Shane