Metadata File Format: Mutation Data

The mutation data metadata file specifies where to find the mutation data files corresponding to each mutation data project.

It must be located at obj/meta-data.tsv

Rows correspond to projects (corresponding to a specific cancer type from a specific source).

It contains the following columns:

• Project: An identifier for the project.
• Project Source: The source of the project.
• Project Name: The project name. Typically named by the cancer type.
• Oncotree Code: A code mapping the cancer type to an Oncotree node.
• Path to Counts SBS_96 File: The path to the counts file corresponding to the SBS_96 category type. Relative to the obj directory.
• Path to Counts DBS_78 File: The path to the counts file corresponding to the DBS_78 category type. Relative to the obj directory.
• Path to Counts INDEL_Alexandrov2018_83 File: The path to the counts file corresponding to the INDEL_Alexandrov2018_83 category type. Relative to the obj directory.
• Path to Clinical File: The path to the clinical data file. Relative to the obj directory. Can be left blank.
• Path to Samples File: The path to the sample-patient mapping file. Relative to the obj directory. Required.
• Path to Genes File: The path to the gene-alterations file. Relative to the obj directory. Can be left blank.

Example:

Project	Project Source	Project Name	Oncotree Code	Path to Counts SBS_96 File	Path to Counts DBS_78 File	Path to Counts INDEL_Alexandrov2018_83 File	Path to Clinical File	Path to Samples File	Path to Genes File
TCGA-BLCA_BLCA_mc3.v0.2.8	TCGA	Bladder Urothelial Carcinoma	BLCA	mutations/PanCanAtlas/processed/counts/counts.TCGA-BLCA_BLCA_mc3.v0.2.8.SBS-96.tsv	mutations/PanCanAtlas/processed/counts/counts.TCGA-BLCA_BLCA_mc3.v0.2.8.DBS-78.tsv	mutations/PanCanAtlas/processed/counts/counts.TCGA-BLCA_BLCA_mc3.v0.2.8.INDEL-Alexandrov2018_83.tsv	clinical/PanCanAtlas/processed/clinical.TCGA_BLCA.tsv	mutations/PanCanAtlas/processed/samples/samples.TCGA-BLCA_BLCA_mc3.v0.2.8.tsv	gene-alterations/mutations/maf/processed/PanCanAtlas-TCGA-BLCA_BLCA_mc3.v0.2.8.tsv
...	...	...	...	...	...	...	...	...	...