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?
I would contact the RTCGAToolbox developers