Exome Seq Training Full W Cached Ref
5.0

Workflow Type: Galaxy

Exome 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

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

gtn star logo followed by the word workflows

Inputs

ID Name Description Type
PEDigree data PEDigree data Family tree with sex and phenotype information in PED format
  • File
father_R1 father_R1 forward reads of the father sample
  • File
father_R2 father_R2 reverse reads of the father sample
  • File
mother_R1 mother_R1 forward reads of the mother sample
  • File
mother_R2 mother_R2 reverse reads of the mother sample
  • File
proband_R1 proband_R1 forward reads of the child/proband sample
  • File
proband_R2 proband_R2 reverse reads of the child/proband sample
  • File

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
  • File
snpeff_variant_stats snpeff_variant_stats n/a
  • File
normalized_snpeff_annotated_variants normalized_snpeff_annotated_variants n/a
  • File
candidate_mutations candidate_mutations n/a
  • File

Version History

5.0 (earliest) Created 2nd Jun 2025 at 11:03 by GTN Bot

Added/updated 4 files


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Created: 2nd Jun 2025 at 11:03

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