Prolem with Dsuite program for introgression test

Question

[reza]

Hi everyone

I have a VCF file including 4 populations (one of that is an outgroup). I used Dsuite program (Dtrios option) for the introgression test. Based on Dsutie paper "The first program, Dtrios calculates the sums in Equation and outputs genome-wide statistics including the D, its associated p-value, and the f4-ratio statistic, for all trios of populations or species". Except for the outgroup, I have three populations and I expected the D statistics to be calculated for all 6 possible trios, while it was calculated for only one trio without any error or warning.

Can anyone help me find the problem?

Thanks

[Ken]

Can you post the contents of your input tree (.nwk) and set (.txt) files here, as well as the output from:

bcftools query -l <your.vcf> ?

This will help diagnose.