BioMuta pipeline README: Difference between revisions
Initial edit |
Download: TCGA |
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== Step 1: Download == | == Step 1: Download == | ||
In the downloader step, mutation lists will be downloaded from each source. Refer to each individual source below for downloading instructions. | In the downloader step, mutation lists will be downloaded from each source. Refer to each individual source below for downloading instructions. | ||
=== Download: TCGA === | |||
There are 2 parts to obtaining data from TCGA: | |||
1. Primary TCGA data | |||
* Available at [https://gdc.cancer.gov/ NCI Genomic Data Commons]. | |||
* Accessible through the ISB-CGC Big Query repository (more info TBA). | |||
2. TCGA controlled-access data | |||
* Hosted at dbGaP. For access, see Sharepoint (link TBA). | |||
=== Download: CIViC === | |||
=== Download: COSMIC === | |||
== Step 2: Convert == | == Step 2: Convert == | ||
Revision as of 15:56, 30 September 2024
This article is still under construction and should not be nominated for deletion.
This page will contain an updated version of this BioMuta documentation page.
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)
- Clinical Interpretation of Variants in Cancer (CIVIC)
- Catalogue of Somatic Mutations in Cancer (COSMIC)
- International Cancer Genome Consortium (ICGC) (retired)
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.
Download: TCGA
There are 2 parts to obtaining data from TCGA:
1. Primary TCGA data
- Available at NCI Genomic Data Commons.
- Accessible through the ISB-CGC Big Query repository (more info TBA).
2. TCGA controlled-access data
- Hosted at dbGaP. For access, see Sharepoint (link TBA).
Download: CIViC
Download: COSMIC
Step 2: Convert
In the convert step, all resources are formatted to the Biomuta standard for both data and field structure.
Step 3: Combine
In the combined step, all resources are combined into a master dataset.