Regions of high linkage disequilibrium (LD)

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.

Chr	Start	Stop	ID
1	48060567	52060567	hild1
2	85941853	100407914	hild2
2	134382738	137882738	hild3
2	182882739	189882739	hild4
3	47500000	50000000	hild5
3	83500000	87000000	hild6
3	89000000	97500000	hild7
5	44500000	50500000	hild8
5	98000000	100500000	hild9
5	129000000	132000000	hild10
5	135500000	138500000	hild11
6	25500000	33500000	hild12
6	57000000	64000000	hild13
6	140000000	142500000	hild14
7	55193285	66193285	hild15
8	8000000	12000000	hild16
8	43000000	50000000	hild17
8	112000000	115000000	hild18
10	37000000	43000000	hild19
11	46000000	57000000	hild20
11	87500000	90500000	hild21
12	33000000	40000000	hild22
12	109521663	112021663	hild23
20	32000000	34500000	hild24
23	14150264	16650264	hild25
23	25650264	28650264	hild26
23	33150264	35650264	hild27
23	55133704	60500000	hild28
23	65133704	67633704	hild29
23	71633704	77580511	hild30
23	80080511	86080511	hild31
23	100580511	103080511	hild32
23	125602146	128102146	hild33
23	129102146	131602146	hild34

Excluding Regions With Plink

You can remove these regions from a PED file using the following PLINK commands. Assuming you have the data stored in a file named "high-ld.txt"

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