A general team for the EOSC4Cancer project.

This file contain the missing copy number information for TracerX study (https://www.nejm.org/doi/full/10.1056/NEJMoa1616288).

EOSC4Cancer_D2.2

Galaxy workflow used for EOSC4Cancer D2.2 - Analytical methods for data extraction, processing and sharing using biomedical images - demonstrator

Link to deliverable report on Zenodo:

The Galaxy workflow for clonal population analysis was designed to process patient mutation data extracted from cBioPortal, specifically using the TracerX study as an example. This workflow, part of the deliverable D3.2 for EOSC4Cancer developed at UiO, begins with a raw patient mutation table from cBioPortal, where modifications and formatting occur to prepare the data for analysis. Some data, notably the copy number alterations (referred to as "All_CN"), were manually uploaded to Galaxy to ...

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 ...

Call somatic, germline and LoH event variants from PE Illumina sequencing data obtained from matched pairs of tumor and normal tissue samples.

This workflow can be used with whole-genome and whole-exome sequencing data as input. For WES data, parts of the analysis can be restricted to the exome capture kits target regions by providing the optional "Regions of Interest" bed dataset.

The current version uses bwa-mem for read mapping and varscan somatic for variant calling and somatic status ...

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.