Entering edit mode
8.8 years ago
yp
▴
10
Hi,
I would like to calculate Theta watterson on SNP data. Could you please suggest me any suitable software?
Thanks, YK
Hi,
I would like to calculate Theta watterson on SNP data. Could you please suggest me any suitable software?
Thanks, YK
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.
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.
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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