Click here to download highld_hg19.txt, a file that contains a list of high-LD regions based on the GRCh37/hg19 assembly, and click here to download highld_hg38.txt, a file that contains a list of high-LD regions based on the GRCh37/hg19 assembly.
We recommend excluding SNPs in high-LD regions when using Principal Component Analysis to detect outliers or construct population covariates. To identify which SNPs are within the high-LD regions, you can use the command --cut-genes (see Gene-based Analysis for more details, or below for an example).
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Example:
Here we use the binary PLINK files human.bed, human.bim and human.fam from the Test Datasets, and the file highld_hg19.txt (download from the top of this page).
Note that the test data files include only Chromosomes 21 & 22, which do not include any high-LD regions. Therefore, for demonstration purposes only, we add a fake region at the start of Chromosome 21, by running
echo "Region25 21 14600000 14700000" | cat highld_hg19.txt - > highld.fake
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To identify which SNPs are within a high-LD region, we run
./ldak.out --cut-genes highld --bfile human --genefile highld.fake
This finds four SNPs (all within the fake high-LD region), which are saved in the file highld/genes.predictors.used.
