Genomic Data Portal (GDC) download a given a link file

Question

[bioinformagician]

Hi, hope the you are doing well.

I want download from https://gdc.cancer.gov/about-data/publications/sarc_2017. The Maf file: Whole exome MAF - genome.wustl.edu_SARC.IlluminaHiSeq_DNASeq_automated.1.5.0.vep.somatic.maf .

Opening the controlled manifest file I see this:

id  file_name   file_size   md5sum
88fed47d-22f8-4ebb-98ca-67842feeaeb8    genome.wustl.edu_SARC.IlluminaHiSeq_DNASeq_automated.1.5.0.vep.somatic.maf  12439054    82819e97ed5892bacdf1ed7382267c04

I understand the interface in R:

# Load required libraries
library(TCGAbiolinks)
library(SummarizedExperiment)
library(org.Hs.eg.db)

query_TCGA <- GDCquery(
  project = "TCGA-SARC",
)

What can I add to the query do download a file given a link? My goal is just to open the maf file with maftools and count the indels for a specific subtype I already have the clinical data and the TCGA id for each patient, just need to download this file really.

Best Regards :)

[Zhenyu Zhang]

download using gdc-client?

Answer 1

[bioinformagician]

Solved using this, then merging all maf files into one. But would like a solution to download that one in specific just to check if it is the same

# Load required libraries
library(TCGAbiolinks)
library(maftools)

# Step 1: Query for MAF file from TCGA-SARC
query_maf <- GDCquery(
  project = "TCGA-SARC",
  data.category = "Simple Nucleotide Variation",
  data.type = "Masked Somatic Mutation",
  workflow.type = "Aliquot Ensemble Somatic Variant Merging and Masking"
)

# Step 2: Download the MAF file
GDCdownload(query_maf)