i really appreciate all the help as i am new to using PLINK.
i am running the below code to generate the distance matrix for a VCF file containing GWAS samples.
plink --vcf input.vcf.gz --distance 1-ibs flat-missing square --double-id --out plinkdistancematrix
the outpur files are
my first problem is that the files dont have a header, and the PLINK documentation does not explain them. so what do the files mean?
my second problem is how to plot the mdist file according to the different populations?
here is a part of the first line from the mdist file. you will see that it doesnt have the sample IDs
0 0.0692113 0.0677864 0.0685928 0.0688168 0.0683407 0.0678936 0.0698271
so what does the file mean and how do i plot it according to the populations?