Cancer variant annotation (hg38 VEP-based)
Version 1

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Run on Galaxy

Workflow Type: Galaxy

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.

SEEK ID: https://workflowhub.eu/workflows/607?version=1

DOI: 10.48546/workflowhub.workflow.607.1

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