Post date: Jul 16, 2020 6:46:47 PM
The information to calculate this using ANGSD is here: http://www.popgen.dk/angsd/index.php/Thetas,Tajima,Neutrality_tests
I need to generate the .pestPG file. :
The .pestPG file is a 14 column file (tab seperated). The first column contains information about the region. The second and third column is the reference name and the center of the window.
We then have 5 different estimators of theta, these are: Watterson, pairwise, FuLi, fayH, L. And we have 5 different neutrality test statistics: Tajima's D, Fu&Li F's, Fu&Li's D, Fay's H, Zeng's E. The final column is the effective number of sites with data in the window.
The format is:
(indexStart,indexStop)(posStart,posStop)(regStat,regStop) chrname wincenter tW tP tF tH tL tajD fulif fuliD fayH zengsE numSites
Follow the tutorial (http://www.popgen.dk/angsd/index.php/Quick_Start) with their data before starting with our data.