Description

Produce a pruned subset of markers that are in approximate linkage equilibrium with each other. Pairs of variants in the current window with squared correlation greater than the threshold are noted and variants are greedily pruned from the window until no such pairs remain.

Input

Name
Description
Pattern

0 ()

1 ()

2 ()

3 ()

window_size (string)

Window size in variant count or kilobase (if the 'kb' modifier is present) units, a variant count to shift the window at the end of each step, and a variance inflation factor (VIF) threshold.

variant_count (string)

Variant count to shift the window at the end of each step.

r2_threshold (string)

Pairwise r2 threshold. At each step, pairs of variants in the current window with squared correlation greater than the threshold are noted, and variants are greedily pruned from the window until no such pairs remain

Output

Name
Description
Pattern

0 ()

0 ()

0 ()

Tools

plink Documentation

Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.

https://www.cog-genomics.org/plink/1.9/devLicense: GPL
Authors