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

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

Author(s)

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

Features

Tutorial
hands_on Identification of somatic and germline variants from tumor and normal sample pairs

Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness purl 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 question
galaxy-download Download
flowchart TD
  0["ℹ️ Input Dataset\nSLGFSK-N_231335_r1_chr5_12_17.fastq"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nSLGFSK-N_231335_r2_chr5_12_17.fastq"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nSLGFSK-T_231336_r1_chr5_12_17.fastq"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Dataset\nSLGFSK-T_231336_r2_chr5_12_17.fastq"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["ℹ️ Input Dataset\nhg19.chr5_12_17.fa"];
  style 4 stroke:#2c3143,stroke-width:4px;
  5["ℹ️ Input Dataset\nhotspots.bed"];
  style 5 stroke:#2c3143,stroke-width:4px;
  6["ℹ️ Input Dataset\ncgi_variant_positions.bed"];
  style 6 stroke:#2c3143,stroke-width:4px;
  7["ℹ️ Input Dataset\n01-Feb-2019-CIVic.bed"];
  style 7 stroke:#2c3143,stroke-width:4px;
  8["ℹ️ Input Dataset\ndbsnp.b147.chr5_12_17.vcf.gz"];
  style 8 stroke:#2c3143,stroke-width:4px;
  9["ℹ️ Input Dataset\nUniprot_Cancer_Genes.13Feb2019.txt"];
  style 9 stroke:#2c3143,stroke-width:4px;
  10["ℹ️ Input Dataset\ncgi_genes.txt"];
  style 10 stroke:#2c3143,stroke-width:4px;
  11["ℹ️ Input Dataset\n01-Feb-2019-GeneSummaries.tsv"];
  style 11 stroke:#2c3143,stroke-width:4px;
  12["FastQC"];
  0 -->|output| 12;
  13["FastQC"];
  1 -->|output| 13;
  14["Trimmomatic"];
  0 -->|output| 14;
  1 -->|output| 14;
  15["FastQC"];
  2 -->|output| 15;
  16["FastQC"];
  3 -->|output| 16;
  17["Trimmomatic"];
  2 -->|output| 17;
  3 -->|output| 17;
  18["FastQC"];
  14 -->|fastq_out_r2_paired| 18;
  19["FastQC"];
  14 -->|fastq_out_r1_paired| 19;
  20["Map with BWA-MEM"];
  14 -->|fastq_out_r1_paired| 20;
  14 -->|fastq_out_r2_paired| 20;
  21["MultiQC"];
  13 -->|text_file| 21;
  15 -->|text_file| 21;
  16 -->|text_file| 21;
  12 -->|text_file| 21;
  22["FastQC"];
  17 -->|fastq_out_r1_paired| 22;
  23["FastQC"];
  17 -->|fastq_out_r2_paired| 23;
  24["Map with BWA-MEM"];
  17 -->|fastq_out_r1_paired| 24;
  17 -->|fastq_out_r2_paired| 24;
  25["Filter"];
  20 -->|bam_output| 25;
  26["MultiQC"];
  19 -->|text_file| 26;
  22 -->|text_file| 26;
  23 -->|text_file| 26;
  18 -->|text_file| 26;
  27["Filter"];
  24 -->|bam_output| 27;
  28["RmDup"];
  25 -->|out_file1| 28;
  29["RmDup"];
  27 -->|out_file1| 29;
  30["BamLeftAlign"];
  28 -->|output1| 30;
  31["BamLeftAlign"];
  29 -->|output1| 31;
  32["CalMD"];
  30 -->|output_bam| 32;
  33["CalMD"];
  31 -->|output_bam| 33;
  34["Filter"];
  32 -->|calmd_output| 34;
  35["Filter"];
  33 -->|calmd_output| 35;
  36["VarScan somatic"];
  34 -->|out_file1| 36;
  35 -->|out_file1| 36;
  37["SnpEff eff:"];
  36 -->|output| 37;
  38["GEMINI load"];
  37 -->|snpeff_output| 38;
  39["GEMINI annotate"];
  36 -->|output| 39;
  38 -->|outfile| 39;
  40["GEMINI annotate"];
  8 -->|output| 40;
  39 -->|outfile| 40;
  41["GEMINI annotate"];
  5 -->|output| 41;
  40 -->|outfile| 41;
  42["GEMINI annotate"];
  7 -->|output| 42;
  41 -->|outfile| 42;
  43["GEMINI annotate"];
  6 -->|output| 43;
  42 -->|outfile| 43;
  44["GEMINI query"];
  43 -->|outfile| 44;
  45["GEMINI query"];
  43 -->|outfile| 45;
  46["GEMINI query"];
  43 -->|outfile| 46;
  47["GEMINI query"];
  43 -->|outfile| 47;
  48["Join"];
  47 -->|outfile| 48;
  9 -->|output| 48;
  49["Join"];
  48 -->|output| 49;
  10 -->|output| 49;
  50["Join"];
  49 -->|output| 50;
  11 -->|output| 50;
  51["Column arrange"];
  50 -->|output| 51;
  1d6fddf0-ce93-414d-a7a3-b09c1d6c5541["Output\ngene_report_output"];
  51 --> 1d6fddf0-ce93-414d-a7a3-b09c1d6c5541;
  style 1d6fddf0-ce93-414d-a7a3-b09c1d6c5541 stroke:#2c3143,stroke-width:4px;

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
  • Click on Workflow on the top menu bar of Galaxy. You will see a list of all your workflows.
  • Click on galaxy-upload Import at the top-right of the screen
  • 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”
  • 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