Workflow Type: Galaxy
Identification of somatic and germline variants from tumor and normal sample pairs tutorial
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 |
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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 |
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cgi_genes.txt | cgi_genes.txt | n/a |
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cgi_variant_positions.bed | cgi_variant_positions.bed | n/a |
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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 |
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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

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Views: 45 Downloads: 4 Runs: 0
Created: 2nd Jun 2025 at 11:03


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