Question: [TCGA] Variant caller used in mutation data of TCGA
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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 (https://portal.gdc.cancer.gov/), 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

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

And the consol give this information,

gdac.broadinstitute.org_BRCA.Clinical_Pick_Tier1.Level_4.2016012800.0.0
gdac.broadinstitute.org_BRCA.Mutation_Packager_Calls.Level_3.2016012800.0.0.tar.gz
trying URL 'http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/BRCA/20160128/gdac.broadinstitute.org_BRCA.Mutation_Packager_Calls.Level_3.2016012800.0.0.tar.gz'
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
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