Thetas,Tajima,Neutrality tests

Angsd can estimate the Tajimas D and other neutrality test. Method works by using the posterior allele frequencies for every site, and uses these for calculating different per-site estimates of theta.

Due to the linearity the population scaled mutation rate is therefore the sum of the per-site estimates

To estimate the thetats do: ./angsd [other input] -realSFS 1 -doThetas 1 -prior prior.sfs.ml The prior is an estimate of the .sfs which can be found using the [RealSFS] method in angsd The output is a file called .thetas.gz To perform the Tajimas D and other related neutralitet tests you should feed the .thetas.gz file into a seperate program called calcstat which can be found in the misc dir of the sourcecode

./calcStat24 -tinput file.thetas.gz -step 50000 -win 50000