Identification of somatic and germline variants from tumor and normal sample pairs tutorial 1.0
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Associated Tutorial
This workflows is part of the tutorial Identification of somatic and germline variants from tumor and normal sample pairs, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Tutorial Author(s): Wolfgang Maier
Tutorial Contributor(s): Verena Moosmann, Simon Gladman, Björn Grüning, Helena Rasche, Bérénice Batut, Wolfgang Maier, Saskia Hiltemann
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| 01-Feb-2019-CIVic.bed | 01-Feb-2019-CIVic.bed | n/a |
|
| 01-Feb-2019-GeneSummaries.tsv | 01-Feb-2019-GeneSummaries.tsv | n/a |
|
| SLGFSK-N_231335_r1_chr5_12_17.fastq | SLGFSK-N_231335_r1_chr5_12_17.fastq | n/a |
|
| SLGFSK-N_231335_r2_chr5_12_17.fastq | SLGFSK-N_231335_r2_chr5_12_17.fastq | n/a |
|
| SLGFSK-T_231336_r1_chr5_12_17.fastq | SLGFSK-T_231336_r1_chr5_12_17.fastq | n/a |
|
| SLGFSK-T_231336_r2_chr5_12_17.fastq | SLGFSK-T_231336_r2_chr5_12_17.fastq | n/a |
|
| Uniprot_Cancer_Genes.13Feb2019.txt | Uniprot_Cancer_Genes.13Feb2019.txt | n/a |
|
| cgi_genes.txt | cgi_genes.txt | n/a |
|
| cgi_variant_positions.bed | cgi_variant_positions.bed | n/a |
|
| dbsnp.b147.chr5_12_17.vcf.gz | dbsnp.b147.chr5_12_17.vcf.gz | n/a |
|
| hg19.chr5_12_17.fa | hg19.chr5_12_17.fa | n/a |
|
| hotspots.bed | hotspots.bed | n/a |
|
Steps
| ID | Name | Description |
|---|---|---|
| 12 | FastQC | toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1 |
| 13 | FastQC | toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1 |
| 14 | Trimmomatic | toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.36.5 |
| 15 | FastQC | toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1 |
| 16 | FastQC | toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1 |
| 17 | Trimmomatic | toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.36.5 |
| 18 | FastQC | toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1 |
| 19 | FastQC | toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1 |
| 20 | Map with BWA-MEM | toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1 |
| 21 | MultiQC | toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.8+galaxy0 |
| 22 | FastQC | toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1 |
| 23 | FastQC | toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1 |
| 24 | Map with BWA-MEM | toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1 |
| 25 | Filter | toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.4.1 |
| 26 | MultiQC | toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.8+galaxy0 |
| 27 | Filter | toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.4.1 |
| 28 | RmDup | toolshed.g2.bx.psu.edu/repos/devteam/samtools_rmdup/samtools_rmdup/2.0.1 |
| 29 | RmDup | toolshed.g2.bx.psu.edu/repos/devteam/samtools_rmdup/samtools_rmdup/2.0.1 |
| 30 | BamLeftAlign | toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.1 |
| 31 | BamLeftAlign | toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.1 |
| 32 | CalMD | toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0.2 |
| 33 | CalMD | toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0.2 |
| 34 | Filter | toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.4.1 |
| 35 | Filter | toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.4.1 |
| 36 | VarScan somatic | toolshed.g2.bx.psu.edu/repos/iuc/varscan_somatic/varscan_somatic/2.4.3.6 |
| 37 | SnpEff eff: | toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1 |
| 38 | GEMINI load | toolshed.g2.bx.psu.edu/repos/iuc/gemini_load/gemini_load/0.20.1+galaxy2 |
| 39 | GEMINI annotate | toolshed.g2.bx.psu.edu/repos/iuc/gemini_annotate/gemini_annotate/0.20.1+galaxy2 |
| 40 | GEMINI annotate | toolshed.g2.bx.psu.edu/repos/iuc/gemini_annotate/gemini_annotate/0.20.1+galaxy2 |
| 41 | GEMINI annotate | toolshed.g2.bx.psu.edu/repos/iuc/gemini_annotate/gemini_annotate/0.20.1+galaxy2 |
| 42 | GEMINI annotate | toolshed.g2.bx.psu.edu/repos/iuc/gemini_annotate/gemini_annotate/0.20.1+galaxy2 |
| 43 | GEMINI annotate | toolshed.g2.bx.psu.edu/repos/iuc/gemini_annotate/gemini_annotate/0.20.1+galaxy2 |
| 44 | GEMINI query | toolshed.g2.bx.psu.edu/repos/iuc/gemini_query/gemini_query/0.20.1+galaxy1 |
| 45 | GEMINI query | toolshed.g2.bx.psu.edu/repos/iuc/gemini_query/gemini_query/0.20.1+galaxy1 |
| 46 | GEMINI query | toolshed.g2.bx.psu.edu/repos/iuc/gemini_query/gemini_query/0.20.1+galaxy1 |
| 47 | GEMINI query | toolshed.g2.bx.psu.edu/repos/iuc/gemini_query/gemini_query/0.20.1+galaxy1 |
| 48 | Join | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.1 |
| 49 | Join | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.1 |
| 50 | Join | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.1 |
| 51 | Column arrange | toolshed.g2.bx.psu.edu/repos/bgruening/column_arrange_by_header/bg_column_arrange_by_header/0.2 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| gene_report_output | gene_report_output | n/a |
|
Version History
master
Creators and Submitter
Views: 242 Downloads: 30 Runs: 0
Created: 2nd Jun 2025 at 11:03
Tags AttributionsNone
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