Theta Watterson on SNP

Question

[yp]

Hi,

I would like to calculate Theta watterson on SNP data. Could you please suggest me any suitable software?

Thanks, YK

Answer 1

[h.mon]

One answer here, another option is dadi.

[yp]

Thanks for the response. I have an SNP file in the VCF format. I am looking for a software which can take SNP as an input. The software you suggested, it takes BAM file as an input. I would like to calculate Theta Watterson using all the SNPs.

Thanks, YK

Answer 2

[Gabriel R.]

I would also suggest ANGSD http://www.popgen.dk/angsd/index.php/Thetas,Tajima,Neutrality_tests if you have access to the original BAM files.

Answer 3

[GabrielMontenegro]

Since you tagged R on your question I would suggest pegas R package. If you want to estimate theta based on the number of segregating sites e.g. SNPs you just have to use: theta.s(s, n) , where s is the number of SNPs and n is the number of sequences.