Cancer variant annotation (hg38 VEP-based) with MAF export
Version 1

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Workflow Type: Galaxy
Stable

A variation of the Cancer variant annotation (hg38 VEP-based) workflow at https://doi.org/10.48546/workflowhub.workflow.607.1.

Like that other workflow it takes a list of tumor/normal sample pair variants in VCF format (see the other workflow for details about the expected format) and

  1. annotates them using the ENSEMBL Variant Effect Predictor and custom annotation data
  2. turns the annotated VCF into a MAF file for import into cBioPortal
  3. generates human-readable variant- and gene-centric reports

In addition, this worklfow exports the resulting MAF dataset to a WebDAV-enabled remote folder for subsequent import into cBioPortal. WebDAV access details can be configured in the Galaxy user preferences.

SEEK ID: https://workflowhub.eu/workflows/629?version=1

DOI: 10.48546/workflowhub.workflow.629.1

Inputs

ID Name Description Type
Annotations data Annotations data n/a
  • File[]
Export folder Export folder n/a
  • string
Report germline variants? Report germline variants? n/a
  • string
Sample metadata Sample metadata n/a
  • File
Study ID Study ID n/a
  • string
Variants to be annotated Variants to be annotated n/a
  • File

Steps

ID Name Description
3 Mutation classes - DO NOT CHANGE toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/1.1.0
7 Create text file toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/1.1.0
8 Predict variant effects toolshed.g2.bx.psu.edu/repos/iuc/ensembl_vep/ensembl_vep/106.1+galaxy1
9 Extract metadata __EXTRACT_DATASET__
10 Select last toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/1.1.0
11 Replace toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3
12 Build list __BUILD_LIST__
13 Cut Cut1
14 Cut Cut1
15 Extract tumor sample ID Cut1
16 Extract normal sample ID Cut1
17 Relabel identifiers __RELABEL_FROM_FILE__
18 Add line to file toolshed.g2.bx.psu.edu/repos/bgruening/add_line_to_file/add_line_to_file/0.1.0
19 Annotation metadata toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3
20 Parse parameter value param_value_from_file
21 Parse parameter value param_value_from_file
22 Sort collection __SORTLIST__
23 Compose text parameter value toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1
24 dbSNP annotations __EXTRACT_DATASET__
25 cancerhotspots data __EXTRACT_DATASET__
26 CIViC variant data __EXTRACT_DATASET__
27 CGI biomarkers __EXTRACT_DATASET__
28 UniProt-annotated cancer genes __EXTRACT_DATASET__
29 CGI-listed genes __EXTRACT_DATASET__
30 CIViC gene data __EXTRACT_DATASET__
31 vcfanno toolshed.g2.bx.psu.edu/repos/iuc/vcfanno/vcfanno/0.3.3+galaxy0
32 bcftools split-vep toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_split_vep/bcftools_plugin_split_vep/1.15.1+galaxy2
33 SnpSift Filter somatic variants toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1
34 SnpSift Filter LOH variant events toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1
35 SnpSift Filter germline variants toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1
36 Build list __BUILD_LIST__
37 Relabel identifiers __RELABEL_FROM_FILE__
38 Convert VCF to MAF toolshed.g2.bx.psu.edu/repos/iuc/vcf2maf/vcf2maf/1.6.21+galaxy1
39 Filter collection __FILTER_FROM_FILE__
40 Extract dataset __EXTRACT_DATASET__
41 Extract dataset __EXTRACT_DATASET__
42 Extract dataset __EXTRACT_DATASET__
43 SnpSift Extract gene-centric Fields toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0
44 SnpSift Extract Fields toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0
45 Replace Text toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3
46 Replace Text toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3
47 Replace Text toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3
48 Replace toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3
49 Replace toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3
50 Build list __BUILD_LIST__
51 Datamash toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0+galaxy2
52 Compute toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0
53 Relabel identifiers __RELABEL_FROM_FILE__
54 Join toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2
55 Replace Text toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3
56 Filter collection __FILTER_FROM_FILE__
57 Join toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2
58 Replace toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3
59 Generate combined MAF of all variants toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0
60 Join toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2
61 Join toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2
62 Generate full variants reports toolshed.g2.bx.psu.edu/repos/bgruening/column_arrange_by_header/bg_column_arrange_by_header/0.2
63 Export datasets export_remote
64 Generate full gene reports toolshed.g2.bx.psu.edu/repos/bgruening/column_arrange_by_header/bg_column_arrange_by_header/0.2
65 Compute toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0
66 Datamash toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0
67 Add line to file toolshed.g2.bx.psu.edu/repos/bgruening/add_line_to_file/add_line_to_file/0.1.0
68 Join toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2
69 Replace Text toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3
70 Split file toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0
71 Filter for known cancer genes Filter1
72 Column arrange toolshed.g2.bx.psu.edu/repos/bgruening/column_arrange_by_header/bg_column_arrange_by_header/0.2
73 Collapse Collection toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2
74 Transpose toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.1.0
75 Column arrange toolshed.g2.bx.psu.edu/repos/bgruening/column_arrange_by_header/bg_column_arrange_by_header/0.2
76 Replace toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3
77 Mutation Summary toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3
78 Replace toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3
79 Replace toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3
80 All somatic variants report __EXTRACT_DATASET__
81 All LoH events report __EXTRACT_DATASET__
82 Collapse Collection toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2
83 Merge collections __MERGE_COLLECTION__
84 Merge collections __MERGE_COLLECTION__
85 Somatic variants report cancer genes __EXTRACT_DATASET__
86 LoH events report cancer genes __EXTRACT_DATASET__
87 Germline variants report cancer genes __EXTRACT_DATASET__
88 Somatic genes summary __EXTRACT_DATASET__
89 LoH genes summary __EXTRACT_DATASET__
90 Germline genes summary __EXTRACT_DATASET__

Outputs

ID Name Description Type
annotation_metadata annotation_metadata n/a
  • File
uniprot_cancer_genes uniprot_cancer_genes n/a
  • File
cgi_genes cgi_genes n/a
  • File
civic_genes civic_genes n/a
  • File
final_variants final_variants n/a
  • File
maf_report maf_report n/a
  • File
variant_reports_tabular variant_reports_tabular n/a
  • File
gene_reports_tabular gene_reports_tabular n/a
  • File
mutations_summary mutations_summary n/a
  • File
somatic_report somatic_report n/a
  • File
loh_report loh_report n/a
  • File
somatic_cancer_report somatic_cancer_report n/a
  • File
loh_cancer_report loh_cancer_report n/a
  • File
germline_cancer_report germline_cancer_report n/a
  • File
gene_cards_somatic gene_cards_somatic n/a
  • File
gene_cards_loh gene_cards_loh n/a
  • File
gene_cards_germline gene_cards_germline n/a
  • File

Version History

Version 1 (earliest) Created 27th Oct 2023 at 16:07 by Wolfgang Maier

Initial commit


Frozen Version-1 1170fa5
help Creators and Submitter
Creator
  • Wolfgang Maier
Submitter
Tools
Variant Effect Predictor (VEP)
vcfanno
SnpSift
cBioPortal
Citation
Maier, W. (2023). Cancer variant annotation (hg38 VEP-based) with MAF export. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.629.1
License
GNU General Public License v3.0 only (GPL-3.0)
Activity

Views: 6494   Downloads: 608   Runs: 2

Created: 27th Oct 2023 at 16:07

Annotated Properties
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Operation annotations
help Attributions

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Total size: 174 KB
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