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

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

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

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