I want to download and analyze the mutation data of TCGA. I find that the mutation data is controlled on original download source (https://portal.gdc.cancer.gov/repository). I search on net and find another source to download the data (http://gdac.broadinstitute.org/runs/stddata__2016_01_28/). This source are from a thread (https://www.biostars.org/p/189418/).
Taking BRCA as example, this is data related to mutation “gdac.broadinstitute.org_BRCA.Mutation_Packager_Calls.Level_3.2016012800.0.0.tar.gz”. I download and unzip it. There are 982 files and one file for one sample.
I find that there are no more than 100 genes with mutations in each file. Why are there so few mutations in each sample?
Where can I download a relative comprehensive mutation dataset of TCGA?