Hoping someone can sanity check my idea.
I’m working on a haploid genome and called SNPs. I want to calculate genome-wise Tajima’s D (I’m sliding windows) using vcftools, but this only works on diploid SNP calls.
If I were to re-call my SNPs in diploid mode, then my SNPs should come up as homozygous diploid, yes? And then I can run vcftools Tajima’s D.
I know there are a few R based tools to do Tajima’s D on haploid data but I’ve had no luck with them and figured I’d try this way instead. Can anyone see any obvious problems?
Thanks, have a good weekend.