13 months ago by
Republic of Ireland
As mentioned, you can obtain the TCGA somatic mutations in Mutation Annotation Format (MAF) from the GDC Legacy Archive - this data is open access, i.e., available to the public. Anyone can download it. To convert MAF to VCF, take a look here: Vcf To Maf (Mutation Annotation Format) Conversion ?
The BAM and VCF files are protected and one requires access permissions granted by the TCGA data access committee. For details of this process, take a look here: Application Process
- the MAF files were produced at different sites (1 file per site) and
using different variant callers
- the same sample may have been processed at more than 1 site
- a single MAF file contains a merged list of variant calls from a
group of patients
- the MAF files each have a filter for 'panel of normals', which
indicates that the somatic variant call was additionally encountered in a panel of
healthy controls sequenced by The Broad Institute of Harvard and MIT.