Changes

There are regions of high linkage diequilibrium in the human genome. These regions should be excluded when performing certain analyses such as principal component analysis on genotype data.

There are regions of long-range, high linkage diequilibrium in the human genome <ref>Price et al. (2008) Long-Range LD Can Confound Genome Scans in Admixed Populations. Am. J. Hum. Genet. 86, 127-147</ref><ref>Weale M. (2010) Quality Control for Genome-Wide Association Studies from Michael R. Barnes and Gerome Breen (eds.), Genetic Variation: Methods and Protocols, Methods in Molecular Biology, vol. 628, DOI 10.1007/978-1-60327-367-1_19, © Springer Science+Business Media, LLC 2010</ref>. These regions should be excluded when performing certain analyses such as principal component analysis on genotype data.

[[File:High-ld.png]]

[[File:High-ld.png]]

     plink --file mydata --make-set high-ld.txt --write-set --out hild

     plink --file mydata --make-set high-ld.txt --write-set --out hild

     plink --file mydata --exclude hild.set --recode --out mydatatrimmed

     plink --file mydata --exclude hild.set --recode --out mydatatrimmed