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• GLM_(PCA).xml

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net.maizegenetics.analysis.workflow.GLM_(PCA).xml Maven / Gradle / Ivy

<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<TasselPipeline>
    <citation>
        Casstevens T, Wang Y. (2015) First Annual Tassel Hackathon.
    </citation>
    <workflow>
        Association analysis using GLM. Population Structure is calculated with PCA.
    </workflow>
    <fork1>
        <importGuess>
            filename
            <workflow> 
                Load Genotype File. (example: mdp_genotype.hmp.txt)
            </workflow>
        </importGuess>
        <filterAlign>
            <filterAlignMinFreq>0.05</filterAlignMinFreq>
            <workflow>
                Filter out mono-morphic sites. (example: Minimum Count: 150, Minimum Frequency: 0.05, Maximum Frequency: 1.0)
            </workflow>
        </filterAlign>
    </fork1>
    <runfork1/>
    <fork2>
        <pca>
            <workflow>
                Using PCA method to calculate the populations structure. (example: number of components: 3)
            </workflow>
        </pca>
        <input1/>
    </fork2>
    <fork3>
        <importGuess>
            filename
            <workflow> 
                Load Phenotypes File. (example: mdp_traits.txt)
            </workflow>
        </importGuess>
    </fork3>
    <runfork3/>
    <combine4>
        <input1/>
        <input2/>
        <input3/>
        <intersect/>
        <glm>
            <workflow>
                Association analysis using GLM.
            </workflow>
        </glm>
        <mhd>
            <workflow>
                Manhattan Plot
                (example: select dpoll to draw the Manhattan plot)
            </workflow>
        </mhd>
    </combine4>
</TasselPipeline>