Calling variants in non-diploid systems

Run Workflow in Galaxy

• Galaxy Europe
• Galaxy France
• Galaxy Main
• Galaxy Australia
• Import to another server (≥23.0+ only!)

flowchart TD
  0["ℹ️ Input Dataset\nraw_child-ds-1.fq"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nraw_child-ds-2.fq"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nraw_mother-ds-1.fq"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Dataset\nraw_mother-ds-2.fq"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["FastQC"];
  0 -->|output| 4;
  5["FastQC"];
  1 -->|output| 5;
  6["Map with BWA-MEM"];
  0 -->|output| 6;
  1 -->|output| 6;
  7["FastQC"];
  2 -->|output| 7;
  8["FastQC"];
  3 -->|output| 8;
  9["Map with BWA-MEM"];
  2 -->|output| 9;
  3 -->|output| 9;
  10["MergeSamFiles"];
  9 -->|bam_output| 10;
  6 -->|bam_output| 10;
  11["MarkDuplicates"];
  10 -->|outFile| 11;
  12["BamLeftAlign"];
  11 -->|outFile| 12;
  13["Filter"];
  12 -->|output_bam| 13;
  14["FreeBayes"];
  13 -->|out_file1| 14;
  15["VCFfilter:"];
  14 -->|output_vcf| 15;
  16["VCFtoTab-delimited:"];
  15 -->|out_file1| 16;
  17["Cut"];
  16 -->|out_file1| 17;
  f2e84a79-a71f-4b5f-a526-55d8cd472a05["Output\ncut_variants"];
  17 --> f2e84a79-a71f-4b5f-a526-55d8cd472a05;
  style f2e84a79-a71f-4b5f-a526-55d8cd472a05 stroke:#2c3143,stroke-width:4px;

Inputs

Outputs

Tools

To use these workflows in Galaxy you can either click the links to download the workflows, or you can right-click and copy the link to the workflow which can be used in the Galaxy form to import workflows.

Importing into Galaxy

Hands-on: Importing a workflow

• Click on Workflow on the top menu bar of Galaxy. You will see a list of all your workflows.
• Click on galaxy-upload Import at the top-right of the screen
• Provide your workflow
  • Option 1: Paste the URL of the workflow into the box labelled “Archived Workflow URL”
  • Option 2: Upload the workflow file in the box labelled “Archived Workflow File”
• Click the Import workflow button

Below is a short video demonstrating how to import a workflow from GitHub using this procedure:

Version History

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/non-dip/workflows/Calling_variants_in_non-diploid_systems.ga -O workflow.ga
workflow-to-tools -w workflow.ga -o tools.yaml
shed-tools install -g GALAXY -a API_KEY -t tools.yaml
workflow-install -g GALAXY -a API_KEY -w workflow.ga --publish-workflows