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GATK analysis using Bam files after BWA alignment

Hello,
I need to perform GATK analyis on my Maize chloroplast samplea. I already generated bam files after aligning data from my samples with reference maize chloroplast genome. My objective is to look foa a single base changes in different samples.
Please provide me the steps to perform the analysis on fire cloud. I do not have any programming skills, so please let me know how I can import GATK analysis files from other workspaces or methods.

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  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @DIWAKER
    Hi,

    Have a look at the FireCloud documentation. They also have a forum and quick start guide which may help.

    -Sheila

  • Thanks Sheila for the reply. However, I do not know how to create a new method in WDL script. Is there a way to import the method from other work space to do Gatk variant analysis of maize plants

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @DIWAKER
    Hi,

    I just moved this question to the FireCloud section where @bshifaw or someone else can help.

    -Sheila

  • bshifawbshifaw moonMember, Broadie, Moderator admin
    edited September 2018

    Like Sheila mentioned, there is a FireCloud user guide for common how to's, including creating a method . Its also possible to copy a method from another workspace or the Method repository which includes several public methods by specifying this when importing a method into a workspace. Please visit the FireCloud Documentation for more details.

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