Hi everyone,

I have been computing Watterson theta for the first time and I am using ANGSD . For my understanding this value can be from 0 to 1. However on ANGSD use likelihood to run it and this is the results I have when I compute theta on Chr22 on one bamfile:

```
(indexStart,indexStop)(firstPos_withData,lastPos_withData)(WinStart,WinStop) Chr WinCenter tW tP tF tH tL Tajima fuf fud fayh zeng nSites
(0,32860927)(16050032,51244307)(0,51244307) 22 25622153 31780.907015 31780.907015 31780.907015 31780.907015 31780.907015 -nan -nan -nan -nan -nan 32860927
```

So what I am interested in is tW (theta Watterson).. but this value means no sense to me. I think I do have to divide it by the nSites which would give me tW=0.0009671336118. Does it make sense to do that ?

I also have the results per sites on a log scale that looks like that:

```
#Chromo Pos Watterson Pairwise thetaSingleton thetaH thetaL
22 16050032 -7.634670 -7.634670 -7.634670 -7.634670 -7.634670
22 16050033 -7.634670 -7.634670 -7.634670 -7.634670 -7.634670
22 16050034 -7.634670 -7.634670 -7.634670 -7.634670 -7.634670
22 16050035 -7.634670 -7.634670 -7.634670 -7.634670 -7.634670
22 16050036 -7.634670 -7.634670 -7.634670 -7.634670 -7.634670
```

Is it better do compute the overall Wtheta using those values ? If yes, should I still do the sum and dividing them by the total number of sites ?

Sorry for the newbie questions, new on this field. Thanks a lot

WIKI: In population genetics, the Watterson estimator is a method for describing the genetic diversity in a population. . So what does it mean on a genomic coordinate level? Maybe theta is each site's contribution. How does it vary across a chromosome?

I think in this way they use the prior knowing the reference true site ? I have no clear idea of it either but this is how I understand it. This is how the value fluctuates, doesn't really make sense to me either:

Hello,

I'm facing the same problem, I have the output of ANGSD and I was wandering how to get the Pi and Theta from the results. Trying to make the average gives me -inf result. Have you find a solution?

Many thanks