Population level theta with saf2theta

[jmhallas]

Hi,

I'm having a difficult time calculating population level theta with saf2theta. Previously, I used doThetas with no issues taking the average of each theta value per site (no window) with thetaStat print ${POP}.thetas.idx > ${POP}.theta_out. When I use thetaStat print on my .idx file from saf2theta the Watterson's theta values for each site are identical.

#Chromo Pos     Watterson       Pairwise        thetaSingleton  thetaH  thetaL
HiCscaffold1000pilon    24356   -1.524667       -1.473819       -inf    -inf    -inf
HiCscaffold1000pilon    27141   -1.524667       -1.907618       -inf    -inf    -inf
HiCscaffold1000pilon    27176   -1.524667       -1.970972       -inf    -inf    -inf

Does anyone have any suggestions on how to calculate population level Watterson's theta and pi using saf2theta thetas.idx.pestPG output?

#(indexStart,indexStop)(firstPos_withData,lastPos_withData)(WinStart,WinStop)   Chr     WinCenter       tW      tP      tF      tH      tL      Tajima  fuf     fud     fayh    zeng    nSites
(0,16)(24356,30946)(0,30946)    HiCscaffold1000pilon    15473   3.483098        2.829233        0.000000        0.000000        0.000000        -0.570743       1.062633        1.699168        0.565453        -0.656416       16
(0,93)(6813,41599)(0,41599)     HiCscaffold1002pilon    20799   20.245506       22.681104       0.000000        0.000000        0.000000        0.420729        1.962157        2.446160        0.816011        -0.706641       93
(0,5)(30657,35749)(0,35749)     HiCscaffold1003pilon    17874   1.088468        1.205675        0.000000        0.000000        0.000000        0.254946        0.982642        1.102553        0.695251        -0.561985       5

Thanks,

Josh