Exome Seq Training Pre-Mapped W Cached Ref 5.0
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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: 1132 Downloads: 193 Runs: 0
Created: 2nd Jun 2025 at 11:03
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