Exome Seq Training Full W Cached Ref 5.0
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Run on GalaxyExome sequencing data analysis for diagnosing a genetic disease
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 |
|---|---|---|---|
| PEDigree data | PEDigree data | Family tree with sex and phenotype information in PED format |
|
| father_R1 | father_R1 | forward reads of the father sample |
|
| father_R2 | father_R2 | reverse reads of the father sample |
|
| mother_R1 | mother_R1 | forward reads of the mother sample |
|
| mother_R2 | mother_R2 | reverse reads of the mother sample |
|
| proband_R1 | proband_R1 | forward reads of the child/proband sample |
|
| proband_R2 | proband_R2 | reverse reads of the child/proband sample |
|
Steps
| ID | Name | Description |
|---|---|---|
| 7 | FastQC | toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0 |
| 8 | FastQC | toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0 |
| 9 | Map with BWA-MEM | toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2 |
| 10 | FastQC | toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0 |
| 11 | FastQC | toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0 |
| 12 | Map with BWA-MEM | toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2 |
| 13 | FastQC | toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0 |
| 14 | FastQC | toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0 |
| 15 | Map with BWA-MEM | toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2 |
| 16 | Samtools view | toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy0 |
| 17 | Samtools view | toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy0 |
| 18 | MultiQC | toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1 |
| 19 | Samtools view | toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy0 |
| 20 | RmDup | toolshed.g2.bx.psu.edu/repos/devteam/samtools_rmdup/samtools_rmdup/2.0.1 |
| 21 | RmDup | toolshed.g2.bx.psu.edu/repos/devteam/samtools_rmdup/samtools_rmdup/2.0.1 |
| 22 | RmDup | toolshed.g2.bx.psu.edu/repos/devteam/samtools_rmdup/samtools_rmdup/2.0.1 |
| 23 | FreeBayes | toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.6+galaxy0 |
| 24 | bcftools norm | toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.15.1+galaxy3 |
| 25 | SnpEff eff: | toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy2 |
| 26 | GEMINI load | toolshed.g2.bx.psu.edu/repos/iuc/gemini_load/gemini_load/0.20.1+galaxy2 |
| 27 | GEMINI inheritance pattern | toolshed.g2.bx.psu.edu/repos/iuc/gemini_inheritance/gemini_inheritance/0.20.1 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| multiqc_input_data | multiqc_input_data | n/a |
|
| 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: 1122 Downloads: 167 Runs: 0
Created: 2nd Jun 2025 at 11:03
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