Cancer variant annotation (hg38 VEP-based)
Version 1

Workflow Type: Galaxy
Stable

This Galaxy workflow takes a list of tumor/normal sample pair variants in VCF 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

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
  • File[]
Report germline variants? Report germline variants? n/a
  • string
Variants to be annotated Variants to be annotated n/a
  • File

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
  • File
dbsnp_vcf dbsnp_vcf n/a
  • File
cancer_hotspots cancer_hotspots n/a
  • File
civic_variants civic_variants n/a
  • File
cgi_biomarkers cgi_biomarkers 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 10th Oct 2023 at 17:08 by Wolfgang Maier

First public version


Frozen Version-1 b12ad30
help Creators and Submitter
Creator
  • Wolfgang Maier
Submitter
Citation
Maier, W. (2023). Cancer variant annotation (hg38 VEP-based). WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.607.1
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Views: 3500   Downloads: 256   Runs: 0

Created: 10th Oct 2023 at 17:08

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