Search and Download

TCGAbiolinks has provided a few functions to download mutation data from GDC. There are two options to download the data:

  1. Use GDCquery_Maf which will download MAF aligned against hg38
  2. Use GDCquery, GDCdownload and GDCpreprare to download MAF aligned against hg19
  3. Use getMC3MAF(), to download MC3 MAF from https://gdc.cancer.gov/about-data/publications/mc3-2017

Mutation data (hg38)

This example will download MAF (mutation annotation files) for variant calling pipeline muse. Pipelines options are: muse, varscan2, somaticsniper, mutect. For more information please access GDC docs.

Mutation data (hg19)

This example will download MAF (mutation annotation files) aligned against hg19 (Old TCGA maf files)

Mutation data MC3 file

This will download the MC3 MAF file from https://gdc.cancer.gov/about-data/publications/mc3-2017, and add project each sample belongs.