Please help with --rel-cutoff
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Maria
Feb 17, 2020, 7:12:50 AM2/17/20
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Dear Chris and all,
As far as I know the default value for --rel-cutoff is 0.025 for getting unrelated individuals. Could you please let me know this value is correspond to which degree of relationship or pihat?
Thanks
Christopher Chang
Feb 17, 2020, 10:07:57 PM2/17/20
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I will instead answer the question you asked on Biostars (“how do I prune second-degree-related samples?”)
“plink2 —bfile ... —king-cutoff 0.088 —make-bed” should work. See https://www.cog-genomics.org/plink/2.0/distance#make_king (and the KING website/paper) for documentation re: kinship values.
—rel-cutoff is obsolete.
“plink2 —bfile ... —king-cutoff 0.088 —make-bed” should work. See https://www.cog-genomics.org/plink/2.0/distance#make_king (and the KING website/paper) for documentation re: kinship values.
—rel-cutoff is obsolete.
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