How to do Tajima's D analysis?

Question

[amitgourav.ghosh12]

Can anyone please suggest how to do Tajima's D analysis and the software required? Or can you please provide me with the links of similar answers. I want to detect signature of positive selection of certain alleles in my database.

[Ram]

Did you try searching in the biostars search engine or Google with +site:biostars.org? I can see related questions in the sidebar. Please show us you've invested some effort.

[amitgourav.ghosh12]

Hello Sir, indeed there are plenty of questions in the site. What I learnt till now is that one can use the package "pegas" in R or use dnasp v.5 or vcf tools for this purpose. I have binary format files from plink and the individuals respective MAFs, but not sequences. I am planning to download vcf tools and try out there if possible.

Thank you!

Answer 1

[xoaib]

You can use this tool called vcf2tajima https://github.com/xoaib4/vcf2tajima

[Mensur Dlakic]

There is nothing wrong in promoting one's own work, but it is customary to disclose the bias when making these recommendations. You may want to make a separate post explaining your tool, rather than adding a note to old threads.