Question: use `plink --rel-cutoff` to remove related samples
0
gravatar for blueskypie
4 weeks ago by
blueskypie40
United States
blueskypie40 wrote:

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 • 109 views
ADD COMMENTlink modified 4 weeks ago by chrchang5235.4k • written 4 weeks ago by blueskypie40
0
gravatar for chrchang523
4 weeks ago by
chrchang5235.4k
United States
chrchang5235.4k wrote:

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.

ADD COMMENTlink written 4 weeks ago by chrchang5235.4k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1712 users visited in the last hour