cBioPortal takes the variant calls from the projects that they host. They just perform their own annotation for consistency.
The TCGA provisional datasets are directly from TCGA data center
partly via Broad Firehose which are updated regularly. We are also
actively curating datasets from literature. Studies from literature
were curated from the data published with the papers. We sometimes
reach out to the investigators to additional data such as clinical
attributes. All the mutation data (VCF or MAF) were processed through
an internal pipeline to annotate the variant effects in a consistent
way across studies.