Description

ADMIXTURE is a program for estimating ancestry in a model-based manner from large autosomal SNP genotype datasets, where the individuals are unrelated (for example, the individuals in a case-control association study).

Input

name:type
description
pattern

meta:map

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

bed_ped_geno:file

One of PLINK “.bed” file or PLINK “.ped” or EIGENSTRAT “.geno” file. If you provide “.bed” then you need to provide “.bim” and “fam” files. If you provide “.ped” or “.geno” then you need to provide a “.map” file and an empty channel.

*.{bed}

bim_map:file

Mandatory accompanying file. One of PLINK “.bim” file or PLINK “.map” file. Provide “.bim” if “.bed” is the input. Provide “.map” if “.ped” or “.geno” is the input.

*.{bim}

fam:file

PLINK “.fam” file. Mandatory if you provide “.bed” as input. Replace with an empty channel if input is “.ped” or “.geno”.

*.{fam}

K:integer

Belief of the number of ancestral populations.

{*}

Output

name:type
description
pattern

ancestry_fractions

meta:map

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

*.Q:file

Space-delimited files containing ancestry fractions. The output filenames have the number of populations (K) that was assumed for the analysis.

*.{Q}

allele_frequencies

meta:map

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

*.P:file

Space-delimited files containing the allele frequencies of the inferred ancestral populations. The output filenames have the number of populations (K) that was assumed for the analysis.

*.{P}

versions

versions.yml:file

File containing software versions

versions.yml

Tools

admixture
Free for Academic Use

ADMIXTURE is a software tool for maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets.

dalexander.github.io/admixture dalexander.github.io/admixture/admixture-manual.pdf 10.1101/gr.094052.109
maintainers
Github user atrigila
Github user gallvp
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