Workflow Type: Galaxy
Frozen
Stable
This Galaxy workflow takes a list of tumor/normal sample pair variants in VCF format and
- annotates them using the ENSEMBL Variant Effect Predictor and custom annotation data
- turns the annotated VCF into a MAF file for import into cBioPortal
- generates human-readable variant- and gene-centric reports
The input VCF is expected to encode somatic status, somatic p-value and germline p-value of each variant in varscan somatic format, i.e., via SS, SPV and GPV INFO keys, respectively.
Inputs
ID | Name | Description | Type |
---|---|---|---|
Annotations data | Annotations data | n/a |
|
Report germline variants? | Report germline variants? | n/a |
|
Variants to be annotated | Variants to be annotated | n/a |
|
Steps
ID | Name | Description |
---|---|---|
2 | Mutation classes - DO NOT CHANGE | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/1.1.0 |
4 | Create text file | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/1.1.0 |
5 | Predict variant effects | toolshed.g2.bx.psu.edu/repos/iuc/ensembl_vep/ensembl_vep/106.1+galaxy1 |
6 | Extract metadata | __EXTRACT_DATASET__ |
7 | Replace | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3 |
8 | Build list | __BUILD_LIST__ |
9 | Cut | Cut1 |
10 | Cut | Cut1 |
11 | Relabel identifiers | __RELABEL_FROM_FILE__ |
12 | Add line to file | toolshed.g2.bx.psu.edu/repos/bgruening/add_line_to_file/add_line_to_file/0.1.0 |
13 | Annotation metadata | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3 |
14 | Sort collection | __SORTLIST__ |
15 | dbSNP annotations | __EXTRACT_DATASET__ |
16 | cancerhotspots data | __EXTRACT_DATASET__ |
17 | CIViC variant data | __EXTRACT_DATASET__ |
18 | CGI biomarkers | __EXTRACT_DATASET__ |
19 | UniProt-annotated cancer genes | __EXTRACT_DATASET__ |
20 | CGI-listed genes | __EXTRACT_DATASET__ |
21 | CIViC gene data | __EXTRACT_DATASET__ |
22 | vcfanno | toolshed.g2.bx.psu.edu/repos/iuc/vcfanno/vcfanno/0.3.3+galaxy0 |
23 | bcftools split-vep | toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_split_vep/bcftools_plugin_split_vep/1.15.1+galaxy2 |
24 | SnpSift Filter somatic variants | toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1 |
25 | SnpSift Filter LOH variant events | toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1 |
26 | SnpSift Filter germline variants | toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1 |
27 | Build list | __BUILD_LIST__ |
28 | Relabel identifiers | __RELABEL_FROM_FILE__ |
29 | Convert VCF to MAF | toolshed.g2.bx.psu.edu/repos/iuc/vcf2maf/vcf2maf/1.6.21+galaxy1 |
30 | Filter collection | __FILTER_FROM_FILE__ |
31 | Extract dataset | __EXTRACT_DATASET__ |
32 | Extract dataset | __EXTRACT_DATASET__ |
33 | Extract dataset | __EXTRACT_DATASET__ |
34 | SnpSift Extract gene-centric Fields | toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0 |
35 | SnpSift Extract Fields | toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0 |
36 | Replace Text | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3 |
37 | Replace Text | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3 |
38 | Replace Text | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3 |
39 | Replace | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3 |
40 | Replace | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3 |
41 | Build list | __BUILD_LIST__ |
42 | Datamash | toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0+galaxy2 |
43 | Compute | toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0 |
44 | Relabel identifiers | __RELABEL_FROM_FILE__ |
45 | Join | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2 |
46 | Replace Text | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3 |
47 | Filter collection | __FILTER_FROM_FILE__ |
48 | Join | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2 |
49 | Replace | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3 |
50 | Generate combined MAF of all variants | toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0 |
51 | Join | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2 |
52 | Join | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2 |
53 | Generate full variants reports | toolshed.g2.bx.psu.edu/repos/bgruening/column_arrange_by_header/bg_column_arrange_by_header/0.2 |
54 | Generate full gene reports | toolshed.g2.bx.psu.edu/repos/bgruening/column_arrange_by_header/bg_column_arrange_by_header/0.2 |
55 | Compute | toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0 |
56 | Datamash | toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0 |
57 | Add line to file | toolshed.g2.bx.psu.edu/repos/bgruening/add_line_to_file/add_line_to_file/0.1.0 |
58 | Join | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2 |
59 | Replace Text | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3 |
60 | Split file | toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0 |
61 | Filter for known cancer genes | Filter1 |
62 | Column arrange | toolshed.g2.bx.psu.edu/repos/bgruening/column_arrange_by_header/bg_column_arrange_by_header/0.2 |
63 | Collapse Collection | toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2 |
64 | Transpose | toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.1.0 |
65 | Column arrange | toolshed.g2.bx.psu.edu/repos/bgruening/column_arrange_by_header/bg_column_arrange_by_header/0.2 |
66 | Replace | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3 |
67 | Mutation Summary | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3 |
68 | Replace | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3 |
69 | Replace | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3 |
70 | All somatic variants report | __EXTRACT_DATASET__ |
71 | All LoH events report | __EXTRACT_DATASET__ |
72 | Collapse Collection | toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2 |
73 | Merge collections | __MERGE_COLLECTION__ |
74 | Merge collections | __MERGE_COLLECTION__ |
75 | Somatic variants report cancer genes | __EXTRACT_DATASET__ |
76 | LoH events report cancer genes | __EXTRACT_DATASET__ |
77 | Germline variants report cancer genes | __EXTRACT_DATASET__ |
78 | Somatic genes summary | __EXTRACT_DATASET__ |
79 | LoH genes summary | __EXTRACT_DATASET__ |
80 | Germline genes summary | __EXTRACT_DATASET__ |
Outputs
ID | Name | Description | Type |
---|---|---|---|
annotation_metadata | annotation_metadata | n/a |
|
dbsnp_vcf | dbsnp_vcf | n/a |
|
cancer_hotspots | cancer_hotspots | n/a |
|
civic_variants | civic_variants | n/a |
|
cgi_biomarkers | cgi_biomarkers | n/a |
|
uniprot_cancer_genes | uniprot_cancer_genes | n/a |
|
cgi_genes | cgi_genes | n/a |
|
civic_genes | civic_genes | n/a |
|
final_variants | final_variants | n/a |
|
maf_report | maf_report | n/a |
|
variant_reports_tabular | variant_reports_tabular | n/a |
|
gene_reports_tabular | gene_reports_tabular | n/a |
|
mutations_summary | mutations_summary | n/a |
|
somatic_report | somatic_report | n/a |
|
loh_report | loh_report | n/a |
|
somatic_cancer_report | somatic_cancer_report | n/a |
|
loh_cancer_report | loh_cancer_report | n/a |
|
germline_cancer_report | germline_cancer_report | n/a |
|
gene_cards_somatic | gene_cards_somatic | n/a |
|
gene_cards_loh | gene_cards_loh | n/a |
|
gene_cards_germline | gene_cards_germline | n/a |
|
Version History
Version 1 (earliest) Created 10th Oct 2023 at 17:08 by Wolfgang Maier
First public version
Frozen
Version-1
b12ad30
Creators and Submitter
Creator
Submitter
Citation
Maier, W. (2023). Cancer variant annotation (hg38 VEP-based). WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.607.1
License
Activity
Views: 3500 Downloads: 256 Runs: 0
Created: 10th Oct 2023 at 17:08
Annotated Properties
Topic annotations
Operation annotations
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