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 (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

bed (file)

PLINK binary biallelic genotype table file

*.{bed}

bim (file)

PLINK extended MAP file

*.{bim}

fam (file)

PLINK sample information file

*.{fam}

window_size (number)

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 (number)

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

*.{}

r2_threshold (number)

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 (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

versions (file)

File containing software versions

versions.yml

prunein (file)

File with IDs of pruned subset of markers that are in approximate linkage equilibrium with each other

*.{prune.in}

pruneout (file)

File with IDs of excluded variants

*.{prune.out}
author
Github user atrigila
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Tools

plink
GPL

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

cog-genomics.org/plink cog-genomics.org/plink/1.9/data https://www.cog-genomics.org/plink/1.9/dev