Question: [TCGA] Variant caller used in mutation data of TCGA
gravatar for thomas00420
8 months ago by
thomas004200 wrote:

Hi, i'm a college student who currently analyzing TCGA mutation data. In GDC data portal (, they provide MAF file of each cancer type(open access files). and this is divided to four files: Mutect, Somaticsniper,Varscan, and MuSE which indicate different variant calling pipeline. However, as i downloaded the mutation data from RTCGAToolbox in R, they did not provide the variant calling information and i want to know which pipeline did they use. below is the code i used

readData = getFirehoseData (dataset="BRCA", runDate="20160128",forceDownload = TRUE,
                          Clinic=TRUE, Mutation=TRUE, Methylation=F, RNASeq2GeneNorm=F)

And the consol give this information,

trying URL ''
Content type 'application/x-gzip' length 10454503 bytes (10.0 MB)

Did they use different variant calling process from the data provided in GDC data portal? then what is it? Where can i find the information about data which RTCGAToolbox provide?

ADD COMMENTlink modified 6 months ago • written 8 months ago by thomas004200

I would contact the RTCGAToolbox developers

ADD REPLYlink written 7 months ago by Kevin Blighe45k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 814 users visited in the last hour