Description

Produce a pruned subset of markers that are in approximate linkage equilibrium with each other.

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 (value)

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 (value)

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

*.{}

variance_inflation_factor (value)

Variance inflation factor (VIF) threshold. At each step, all variants in the current window with VIF exceeding the threshold are removed.

*.{}

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}
maintainer
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