diploid 4.0
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Run on GalaxyCalling variants in diploid systems
Associated Tutorial
This workflows is part of the tutorial Calling variants in diploid systems, available in the GTN
Features
- Includes Galaxy Workflow Tests
- Includes a Galaxy Workflow Report
Thanks to...
Workflow Author(s): Anton Nekrutenko, Nicola Soranzo
Tutorial Author(s): Anton Nekrutenko, Nicola Soranzo, Khaled Jum'ah
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| GIAB-Ashkenazim-Trio-hg19.bam | #main/GIAB-Ashkenazim-Trio-hg19.bam | Bam file |
|
| GIAB-Ashkenazim-Trio.tabular | #main/GIAB-Ashkenazim-Trio.tabular | n/a |
|
Steps
| ID | Name | Description |
|---|---|---|
| 2 | FreeBayes | toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.9+galaxy0 |
| 3 | VcfAllelicPrimitives: | toolshed.g2.bx.psu.edu/repos/devteam/vcfallelicprimitives/vcfallelicprimitives/1.0.0_rc3+galaxy0 |
| 4 | SnpEff eff: | toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/5.2+galaxy0 |
| 5 | GEMINI load | toolshed.g2.bx.psu.edu/repos/iuc/gemini_load/gemini_load/0.20.1+galaxy2 |
| 6 | GEMINI_query2 | toolshed.g2.bx.psu.edu/repos/iuc/gemini_query/gemini_query/0.20.1+galaxy2 |
| 7 | GEMINI_db_info | toolshed.g2.bx.psu.edu/repos/iuc/gemini_db_info/gemini_db_info/0.20.1 |
| 8 | GEMINI_query1 | toolshed.g2.bx.psu.edu/repos/iuc/gemini_query/gemini_query/0.20.1+galaxy2 |
Version History
master
Creators and Submitter
Views: 1194 Downloads: 167 Runs: 0
Created: 2nd Jun 2025 at 11:02
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Related items
Teams: Galaxy Training Network
Organizations: Galaxy
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Galaxy is an open, web-based platform for accessible, reproducible, and transparent computational biological research.
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The Galaxy Training Network (GTN) is a collection of hands-on tutorials that are designed to be interactive and are built around Galaxy.
These tutorials can be used for learning and teaching how to use Galaxy for general data analysis, as well as a wide array of hands-on tutorials covering specific domains such as assembly, RNA-Seq analysis, deep learning, climate analysis, and more!
