BioMuta Pipeline v-5.0 README
Last Updated August 2022 by Ned Cauley
Description
The Biomuta pipeline gathers mutation data from various sources and combines them into a single dataset under common field structure.
The sources included in BioMuta are:
The Cancer Genome Atlas (TCGA) : https://www.cancer.gov/about-nci/organization/ccg/research/structural-genomics/tcga
International Cancer Genome Consortium (ICGC) : https://dcc.icgc.org/
Clinical Interpretation of Variants in Cancer (CIVIC) : https://civicdb.org/welcome
Catalogue of Somatic Mutations in Cancer (COSMIC) : https://cancer.sanger.ac.uk/cosmic
BioMuta gathers mutation data for the following cancers:
Urinary Bladder Cancer (DOID:11054)
Breast Cancer (DOID:1612)
Colorectal (DOID:9256)
Esophageal Cancer (DOID:5041)
Head and Neck Cancer (DOID:11934)
Kidney Cancer (DOID:263)
Liver Cancer (DOID:3571)
Lung Cancer (DOID:1324)
Prostate Cancer (DOID:10283)
Stomach Cancer (DOID:10534)
Thyroid Gland Cancer (DOID:1781)
Uterine Cancer (DOID:363)
Cervical Cancer (DOID:4362)
Brain Cancer (DOID:1319)
Hematologic Cancer (DOID:2531)
Adrenal Gland Cancer (DOID:3953)
Pancreatic Cancer (DOID:1793)
Ovarian Cancer (DOID:2394)
Skin Cancer (DOID:4159)
Running the Pipeline
To run the BioMuta pipeine, download the scripts from the HIVE Lab github repo: GW HIVE BioMuta Repository
Pipeline Overview
Step 1: Download
In the downloader step, mutation lists will be downloaded from each source. Refer to each individual source below for downloading instructions.
Note
An account is needed for the resources TCGA and COSMIC (see download pages for more info).
Sample name (ID) is available for the resources TCGA and COSMIC
Index for download step:
Step 2: Convert
In the convert step, all resources are formatted to the Biomuta standard for both data and field structure.
Index for convert step:
Step 3: Combine
In the combined step, all resources are combined into a master dataset.
Index for combined step: