Workflow Type: Galaxy
Exome 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

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Views: 41 Downloads: 3 Runs: 0
Created: 2nd Jun 2025 at 11:03


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