Exome Seq Training Pre-Mapped W Cached Ref 5.0
Visit source
Download RO-Crate
Run on GalaxyExome sequencing data analysis for diagnosing a genetic disease; short version starting from pre-mapped reads
Associated Tutorial
This workflows is part of the tutorial Exome sequencing data analysis for diagnosing a genetic disease, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Workflow Author(s): Wolfgang Maier
Tutorial Author(s): Wolfgang Maier, Bérénice Batut, Torsten Houwaart, Anika Erxleben, Björn Grüning
Tutorial Contributor(s): Saskia Hiltemann, Björn Grüning, Nicola Soranzo, Helena Rasche, Bérénice Batut, Wolfgang Maier, Gildas Le Corguillé, Ekaterina Polkh, Martin Čech, Niall Beard, Armin Dadras, Teresa Müller
Funder(s): ELIXIR Europe, de.NBI, University of Freiburg
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Father data | Father data | Pre-mapped reads of the father sample |
|
| Mother data | Mother data | Pre-mapped reads of the mother sample |
|
| PEDigree data | PEDigree data | Family tree with sex and phenotype information in PED format |
|
| Proband data | Proband data | Pre-mapped reads of the child/proband sample |
|
Steps
| ID | Name | Description |
|---|---|---|
| 4 | Samtools view | toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy0 |
| 5 | Samtools view | toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy0 |
| 6 | Samtools view | toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy0 |
| 7 | RmDup | toolshed.g2.bx.psu.edu/repos/devteam/samtools_rmdup/samtools_rmdup/2.0.1 |
| 8 | RmDup | toolshed.g2.bx.psu.edu/repos/devteam/samtools_rmdup/samtools_rmdup/2.0.1 |
| 9 | RmDup | toolshed.g2.bx.psu.edu/repos/devteam/samtools_rmdup/samtools_rmdup/2.0.1 |
| 10 | FreeBayes | toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.6+galaxy0 |
| 11 | bcftools norm | toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.15.1+galaxy3 |
| 12 | SnpEff eff: | toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy2 |
| 13 | GEMINI load | toolshed.g2.bx.psu.edu/repos/iuc/gemini_load/gemini_load/0.20.1+galaxy2 |
| 14 | GEMINI inheritance pattern | toolshed.g2.bx.psu.edu/repos/iuc/gemini_inheritance/gemini_inheritance/0.20.1 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| snpeff_variant_stats | snpeff_variant_stats | n/a |
|
| normalized_snpeff_annotated_variants | normalized_snpeff_annotated_variants | n/a |
|
| candidate_mutations | candidate_mutations | n/a |
|
Version History
master
Creators and Submitter
Views: 1318 Downloads: 217 Runs: 0
Created: 2nd Jun 2025 at 11:03
Tags AttributionsNone
Related items
Teams: Galaxy Training Network
Organizations: Galaxy
I'm a bot managed by @hexylena to upload workflows from the Galaxy Training Network to the WorkflowHub. If you have any issues with my behaviour please let her know by filing an issue.
Galaxy is an open, web-based platform for accessible, reproducible, and transparent computational biological research.
- Accessible: Users can easily run tools without writing code or using the CLI; all via a user-friendly web interface.
- Reproducible: Galaxy captures all the metadata from an analysis, making it completely reproducible.
- Transparent: Users share and publish analyses via interactive pages that can enhance analyses with user annotations.
- Scalable: Galaxy can run ...
Teams: Galaxy Training Network, usegalaxy-eu, Intergalactic Workflow Commission (IWC)
Web page: https://galaxyproject.org/
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!
