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use `plink --rel-cutoff` to remove related samples

In the plink --rel-cutoff option, the default value for genomic relateness is 0.025. How does this genomic relateness value correspond to the degree of relationship or the PI-HAT?

Thanks for any help!

plink
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updated by Kevin Blighe Kevin Blighe • written by blueskypie • blueskypie

1 answer

It is the relationship coefficient described in the GCTA paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3014363/

Note that plink 2.0's --king-cutoff function is a more reliable way to prune close relationships, since it doesn't require good population allele frequencies.

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written by chrchang523 chrchang523

Hi chrchang523,

Although it's late, I read the corresponding paper; but the question is still remaining. Could you please let me know which value should be selected for --rel-cutoff for removing related individuals with 2th degree of relationship?

Thanks

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written by seta seta

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