Computing Tajima's D from haploid SNPs

Question

[drowl1]

Hi all!

I have a set of haploid SNPs that I would like to compute their Tajima's D and it appears that my first choice tool VCFtools only computes this value for diploid data.

Has anyone worked around this challenge before, or is there some other tool that can easily compute Tajima's D on haploid SNPs?

[grant.hovhannisyan]

I am not 100% sure, but maybe DNAsp6 can do than http://www.ub.edu/dnasp/DnaSP6_Documentation_6.12.pdf

[rohitsatyam102]

I am doomed. Vcftools doesn't have --haploid option anymore and DnaSP6 is not available. Is there another tool for haploid organisms.

Answer 1

[Prash]

Yes, it is because of annuling haplotype caller paving way for unified genotyper

I tried tweaking, in vain. Bcftools has other option though.