This document describes the output produced by the pipeline. Most of the plots are taken from the MultiQC report, which summarises results at the end of the pipeline.
The pipeline is built using Nextflow and processes data using the following steps:
- VEP - Variant effect prediction via Ensembl VEP
- Report Generation - Aggregate clinical variant annottion report
VEP is used to annotate raw VCF files. The annotation includes the predicted effects of the mutations on the protein function.
Output directory: results
<VCF>.vcf- Annotated VCF file
Report Generation processes the information found in the annotated VCF file and conducts further annotations including driver gene type and therapeutic suggestions. The resulting json report includes 6 main categories:
- "mskdg": Somatic Mutations in Known Driver genes
List of cancer driver genes along with the observed mutations in the patient. - "ptp_da": Summary of Cancer Drugs Targeting the Affected genes
List of cancer drugs targeting the mutated gene. - "ptp_ia": CIViC Summary of Drugs Targeting the Affected genes
Therapies that have evidence of targeting the affected gene - "mskpe": Somatic Mutations with Known Pharmacogenetic Effect List of drugs that directly targets the observed variant of the gene
- "ref": References
The publications as an evidence of the found annotation/information - "appendix": Appendix
All the somatic variants of the patient with their dbSNP and COSMIC IDs.
Output directory: results
<REPORT>.json- Clinical report in json format.