Hi all! I'm having problems with .evec file when running smartPCA. This file doesn't consider all the individuals that I introduced in .ped file (529 individuals).
Anyone knows what the problem might be? The command that I used was: ./smartpca -p Patag_sud_maf_ld.par > Patag_sud_maf_ld.out
The .par file contains:
genotypename: Patag_sud_maf_ld.ped snpname: Patag_sud_maf_ld.map indivname: Patag_sud_maf_ld.ped evecoutname: Patag_sud_maf_ld.evec evaloutname: Patag_sud_maf_ld.eval numoutlieriter: 0
I will apreciate your answer!