DivAssociate is a workflow implemented in Nextflow to perform a GWAS using GEMMA's [1] Linear Mixed Model algorithm. It uses genotyping data in VCF format and phenotyping data in a CSV file.

Worfklow visualization

flowchart TB
    subgraph " "
    v0["vcfFile"]
    v1["sampleFile"]
    v4["phenotypeFile"]
    end
    v2([prepareVcf])
    v3([transformVcfToPlink])
    v5([preparePhenotypes])
    v6([combineFamWithPhenotypes])
    v7([computeRelatednessMatrix])
    v8([performAssocTest])
    v9([plotOverview])
    subgraph " "
    v10[" "]
    v14[" "]
    end
    v11([splitChromosome])
    v13([plotChromosomewide])
    v12(( ))
    v0 --> v2
    v1 --> v2
    v2 --> v3
    v3 --> v7
    v3 --> v6
    v3 --> v8
    v4 --> v5
    v5 --> v6
    v6 --> v7
    v6 --> v8
    v7 --> v8
    v8 --> v9
    v8 --> v11
    v9 --> v10
    v11 --> v12
    v12 --> v13
    v13 --> v14

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Citations

[1] Zhou, X., Stephens, M. Genome-wide efficient mixed-model analysis for association studies. Nat Genet 44, 821–824 (2012). https://doi.org/10.1038/ng.2310

[2] Li H. A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics. 2011 Nov 1;27(21):2987-93. doi: 10.1093/bioinformatics/btr509. Epub 2011 Sep 8. PMID: 21903627; PMCID: PMC3198575.

[3] Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M. A., Bender, D., ... & Sham, P. C. (2007). PLINK: a tool set for whole-genome association and population-based linkage analyses. The American journal of human genetics, 81(3), 559-575.

[4] Felipe da Veiga Leprevost, Björn A Grüning, Saulo Alves Aflitos, Hannes L Röst, Julian Uszkoreit, Harald Barsnes, Marc Vaudel, Pablo Moreno, Laurent Gatto, Jonas Weber, Mingze Bai, Rafael C Jimenez, Timo Sachsenberg, Julianus Pfeuffer, Roberto Vera Alvarez, Johannes Griss, Alexey I Nesvizhskii, Yasset Perez-Riverol, BioContainers: an open-source and community-driven framework for software standardization, Bioinformatics, Volume 33, Issue 16, August 2017, Pages 2580–2582, https://doi.org/10.1093/bioinformatics/btx192