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Watterson theta estimate

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

population-genetics snp
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updated by Ram Ram • written by Ripeapple • Ripeapple

1 answer

I highly recommend:

https://github.com/ANGSD/angsd

Here is the wiki for Theta:

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

• 0 views • link
updated by Ram Ram • written by Zev.Kronenberg Zev.Kronenberg

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