Du Novo GTN Tutorial - Variant Calling

variant-analysis-dunovo/variant-calling

Author(s)

Version
3
Last updated
Jan 17, 2020
License
None Specified, defaults to CC-BY-4.0
Tags
variant-analysis

Features
Tutorial
Calling very rare variants
Other workflows associated with this material
Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00259
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on WorkflowHub
Launch in Tutorial Mode
Download 
flowchart TD
  0["ℹ️ Input Dataset\nTrimmed reads mate 1"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nTrimmed reads mate 2"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["Map with BWA-MEM"];
  0 -->|output| 2;
  1 -->|output| 2;
  3["BamLeftAlign"];
  2 -->|bam_output| 3;
  4["Naive Variant Caller NVC"];
  3 -->|output_bam| 4;
  5["Variant Annotator"];
  4 -->|output_vcf| 5;
  6["Filter"];
  5 -->|output| 6;

Inputs

Input Label
Input dataset Trimmed reads (mate 1)
Input dataset Trimmed reads (mate 2)

Outputs

From Output Label
Input dataset Trimmed reads (mate 1)
Input dataset Trimmed reads (mate 2)
toolshed.g2.bx.psu.edu/repos/nick/allele_counts/allele_counts_1/1.2 Variant Annotator
Filter1 Filter

Tools

Tool Links
Filter1
toolshed.g2.bx.psu.edu/repos/blankenberg/naive_variant_caller/naive_variant_caller/0.0.4 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.1.0.46-0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/nick/allele_counts/allele_counts_1/1.2 View in ToolShed

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

Below are the instructions for importing these workflows directly into your Galaxy server of choice to start using them!
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 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:

Video: Importing a workflow from URL

Version History

Version Commit Time Comments
3 eb4d724e0 2020-01-15 10:41:35 Workflow renaming
2 361236c41 2019-04-04 09:00:14 Changed format of workflows
1 769796807 2018-07-27 03:28:37 Update rare variant calling tutorial for GTN consistency and new tool version. - Format to be more consistent with other GTN tutorials. - Update to work with newer version of Du Novo (2.15 instead of 0.3). - Restructure logic and flow, add more explanations. - Add workflow files.

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/dunovo/workflows/variant-calling.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