Watterson theta estimate

Question

[Ripeapple]

Hello,

I have the SNP genotype data for about 500 individuals which belong to 30 populations. I am interested in estimating the Watterson's theta and effective population size, I understand knowing one of them can infer the other. I am wondering if anyone can recommend any command line program or software to do the job,

Thanks a lot for any help,

Mandy

Answer 1

[Zev.Kronenberg]

I highly recommend:

https://github.com/ANGSD/angsd

Here is the wiki for Theta:

http://www.popgen.dk/angsd/index.php/Tajima