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

]

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 (value)

Belief of the number of ancestral populations.

{*}

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

Q-ancestry-fractions (file)

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

*.{Q}

P-allele-frequencies (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}
author
Github user atrigila
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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