Workflow Type: Galaxy
Open
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 tutorial, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Tutorial Author(s): Wolfgang Maier
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 |
|
cgi_genes.txt | cgi_genes.txt | n/a |
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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
1.0 (earliest) Created 25th Jun 2024 at 10:55 by Helena Rasche
Added/updated 4 files
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Views: 134 Downloads: 47
Created: 25th Jun 2024 at 10:55
Last updated: 25th Jun 2024 at 10:55
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