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:false ]

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: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:type
description
pattern

prunein

meta:map

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

*.prune.in:file

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

*.{prune.in}

pruneout

meta:map

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

*.prune.out:file

File with IDs of excluded variants

*.{prune.out}

versions

versions.yml:file

File containing software versions

versions.yml

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
Github user atrigila
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