Easy GDC MAF file concatenation
The GDC MAF Concatenation Tool automatically downloads a set of open-access MAFs from the Genomic Data Commons and concatenates them. Each subset of MAFs can be specified using a manifest downloaded from the GDC Data Portal (https://portal.gdc.cancer.gov) or using project IDs.
Either a manifest (-m) or project (-p) must be specified. More than one project can be specified by passing a comma-delimited string with no spaces; i.e. TCGA-LUAD,TCGA-LUSC
Each file downloaded is checked automatically for integrity by comparing the observed (file) and expected (API) md5sum.
usage: python gdc-maf-cat.py <-m MANIFEST or -p PROJECT_ID>
----GDC MAF Concatenation Tool v1.0----
optional arguments:
-h, --help show this help message and exit
-m MANIFEST, --manifest MANIFEST Specify MAF files with GDC Manifest
-p PROJECT, --project PROJECT Specify MAF files by project
-o FILE_PREFIX, --output FILE_PREFIX Designates a name for the output file