Hi, the CONVERTF program in EIGENSOFT package is ignoring few samples and not calculating their principal components.
I am seeing this in my terminal when executing CONVERTF.
genetic distance set from physical distance
genotype file processed
numvalidind: 21 maxmiss: 21001
##end of convertf run
Usually, it says ignoring all samples and then outputs the principal components for all the samples. I am just inputting the .PED and .MAP files in par.PED.EIGENSTRAT. It'd be great if anybody can give me some insight on this.