Interpreting theta value

Question

[yolek64754]

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

[karl.stamm]

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?

[yolek64754]

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:

-7.634670
-7.634670
-7.634670
-7.634670
-7.634670
-7.634670
-7.634670
-7.634670
-7.634670
-8.327583
-8.327583
-8.327583
-8.327583
-8.327583
-8.327583
-8.327583
-8.327583
-8.327583
-8.327583
-8.327583
-8.327583
-8.327583
-8.327583
-8.327583
-8.327583
-8.327583
-8.327583
-8.327583
-9.020618
-9.020618
-8.327583
-9.020618
-9.020618
-9.020618
-9.020618

[Alice]

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