Remove related samples using plink
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.
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