Exome Seq Training Full W Cached Ref
5.0

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Workflow Type: Galaxy

Exome sequencing data analysis for diagnosing a genetic disease

Associated Tutorial

This workflows is part of the tutorial Exome Seq Training Full W Cached Ref, available in the GTN

Features

Thanks to...

Tutorial Author(s): Wolfgang Maier, Bérénice Batut, Torsten Houwaart, Anika Erxleben, Björn Grüning

Workflow Author(s): Wolfgang Maier

gtn star logo followed by the word workflows

SEEK ID: https://dev.workflowhub.eu/workflows/1114?version=1

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 25th Jun 2024 at 10:59 by Helena Rasche

Added/updated 4 files


Open master f99fb96
help Creators and Submitter
Creators
Not specified
Submitter
Discussion Channel
GTN Matrix
Tools
FastQC
BWA
SAMtools
MultiQC
FreeBayes
BCFtools
GEMINI
License
MIT License
Activity

Views: 404   Downloads: 115

Created: 25th Jun 2024 at 10:58

Last updated: 25th Jun 2024 at 10:59

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