Identification of somatic and germline variants from tumor and normal sample pairs tutorial

variant-analysis-somatic-variants/somatic-variants-tutorial-workflow

Author(s)

Version
1
Last updated
Oct 10, 2020
License
None Specified, defaults to CC-BY-4.0
Tags
variant-analysis

Features
Tutorial
Identification of somatic and germline variants from tumor and normal sample pairs
Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00268
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on (Dev) WorkflowHub
Launch in Tutorial Mode
Download 
output
output
output
output
output
output
output
output
fastq_out_r2_paired
fastq_out_r1_paired
fastq_out_r1_paired
fastq_out_r2_paired
text_file
text_file
text_file
text_file
fastq_out_r1_paired
fastq_out_r2_paired
fastq_out_r1_paired
fastq_out_r2_paired
bam_output
text_file
text_file
text_file
text_file
bam_output
out_file1
out_file1
output1
output1
output_bam
output_bam
calmd_output
calmd_output
out_file1
out_file1
output
snpeff_output
output
outfile
output
outfile
output
outfile
output
outfile
output
outfile
outfile
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ℹ️ Input Dataset
SLGFSK-N_231335_r1_chr5_12_17.fastq
ℹ️ Input Dataset
SLGFSK-N_231335_r2_chr5_12_17.fastq
ℹ️ Input Dataset
SLGFSK-T_231336_r1_chr5_12_17.fastq
ℹ️ Input Dataset
SLGFSK-T_231336_r2_chr5_12_17.fastq
ℹ️ Input Dataset
hg19.chr5_12_17.fa
ℹ️ Input Dataset
hotspots.bed
ℹ️ Input Dataset
cgi_variant_positions.bed
ℹ️ Input Dataset
01-Feb-2019-CIVic.bed
ℹ️ Input Dataset
dbsnp.b147.chr5_12_17.vcf.gz
ℹ️ Input Dataset
Uniprot_Cancer_Genes.13Feb2019.txt
ℹ️ Input Dataset
cgi_genes.txt
ℹ️ Input Dataset
01-Feb-2019-GeneSummaries.tsv
FastQC
FastQC
Trimmomatic
FastQC
FastQC
Trimmomatic
FastQC
FastQC
Map with BWA-MEM
MultiQC
FastQC
FastQC
Map with BWA-MEM
Filter
MultiQC
Filter
RmDup
RmDup
BamLeftAlign
BamLeftAlign
CalMD
CalMD
Filter
Filter
VarScan somatic
SnpEff eff:
GEMINI load
GEMINI annotate
GEMINI annotate
GEMINI annotate
GEMINI annotate
GEMINI annotate
GEMINI query
GEMINI query
GEMINI query
GEMINI query
Join
Join
Join
Column arrange
Output
gene_report_output

Inputs

Input Label
SLGFSK-N_231335_r1_chr5_12_17.fastq SLGFSK-N_231335_r1_chr5_12_17.fastq
SLGFSK-N_231335_r2_chr5_12_17.fastq SLGFSK-N_231335_r2_chr5_12_17.fastq
SLGFSK-T_231336_r1_chr5_12_17.fastq SLGFSK-T_231336_r1_chr5_12_17.fastq
SLGFSK-T_231336_r2_chr5_12_17.fastq SLGFSK-T_231336_r2_chr5_12_17.fastq
hg19.chr5_12_17.fa hg19.chr5_12_17.fa
hotspots.bed hotspots.bed
cgi_variant_positions.bed cgi_variant_positions.bed
01-Feb-2019-CIVic.bed 01-Feb-2019-CIVic.bed
dbsnp.b147.chr5_12_17.vcf.gz dbsnp.b147.chr5_12_17.vcf.gz
Uniprot_Cancer_Genes.13Feb2019.txt Uniprot_Cancer_Genes.13Feb2019.txt
cgi_genes.txt cgi_genes.txt
01-Feb-2019-GeneSummaries.tsv 01-Feb-2019-GeneSummaries.tsv

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/bgruening/column_arrange_by_header/bg_column_arrange_by_header/0.2 Column arrange

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/bgruening/column_arrange_by_header/bg_column_arrange_by_header/0.2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.4.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0.2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/samtools_rmdup/samtools_rmdup/2.0.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/gemini_annotate/gemini_annotate/0.20.1+galaxy2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/gemini_load/gemini_load/0.20.1+galaxy2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/gemini_query/gemini_query/0.20.1+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.8+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/varscan_somatic/varscan_somatic/2.4.3.6 View in ToolShed
toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.36.5 View in ToolShed

To use these workflows in Galaxy you can either click the links to download the workflows, or you can right-click and copy the link to the workflow which can be used in the Galaxy form to import workflows.

Importing into Galaxy

Below are the instructions for importing these workflows directly into your Galaxy server of choice to start using them!
Hands On: Importing a workflow
  1. Click on Workflows in the Galaxy activity bar (on the left side of the screen, or in the top menu bar of older Galaxy instances). You will see a list of all your workflows
  2. Click on Import at the top-right of the screen
  3. Provide your workflow
    • Option 1: Paste the URL of the workflow into the box labelled “Archived Workflow URL”
    • Option 2: Upload the workflow file in the box labelled “Archived Workflow File”
  4. Click the Import workflow button

Below is a short video demonstrating how to import a workflow from GitHub using this procedure:

Video: Importing a workflow from URL

Version History

Version Commit Time Comments
1 caffacad4 2020-10-10 20:50:51 Somatic variants tutorial updates (#2054)

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/somatic-variants/workflows/somatic_variants_tutorial_workflow.ga -O workflow.ga
workflow-to-tools -w workflow.ga -o tools.yaml
shed-tools install -g GALAXY -a API_KEY -t tools.yaml
workflow-install -g GALAXY -a API_KEY -w workflow.ga --publish-workflows