I generated pairwise IBD (PI_HAT) using plink1.9 --genome option. I have >200,000 samples, so I used --parallel and combined the sub files using cat. Is there a way to remove related samples using the output file .genome.gz ?
I read about --rel-cutoff but this option is generating IBD measures from scratch and cannot be used with --parallel as I understood. Another way I found to do this is:
plink2 --bfile inputfile --make-king triangle bin --out related
plink2 --bfile inputfile --king-cutoff related 0.125 --make-bed --out unrelated
I have 3 things to clarify. 1) Is this the correct way? 2) Is there anyway that I can use my initial output from --genome to remove related individuals? This file is big since I have >200,000 samples 2) In my initial QC steps I used plink1.9, I assume I can use plink2 with the same outputs.
Thanks a lot in advance. Sumudu