Why do some open-access masked somatic MAF files not contain variants?

Answer: 

Tumor mutational frequency is affected by a number of factors including cancer type, tissue status, and patient age. Because the open-access masked somatic MAF data are heavily filtered to remove potential germline variants (for more information see: https://docs.gdc.cancer.gov/Data/File_Formats/MAF_Format/), there are instances where these files may not contain low frequency somatic variants. If omission of true-positive somatic mutations is a concern, we recommend accessing controlled-access MAFs through GDC, which requires user certification through dbGaP. copy number variation and structural rearrangement data files are also generated and may be useful to the end user.

Two examples of GDC open-access masked somatic MAF files with no called variants are:

ID3 Sample Type URL File Name
HCM-BROD-0036-C41 Metastatic https://portal.gdc.cancer.gov/files/95630c4c-da94-45f5-af53-a1359b573399 19ae9397-2571-4cd4-ba6c-591a3c9d9514.wxs.aliquot_ensemble_masked.maf.gz
HCM-CSHL-0093-C25 Primary Tumor https://portal.gdc.cancer.gov/files/4a29645b-6f99-4e90-84fe-6cb731801308 15ea5804-8b47-4689-9db8-29c794e50436.wxs.aliquot_ensemble_masked.maf.gz

 

Associated Program: 
Human Cancer Models Initiative
PGDI: 
No
Last updated: April 21, 2021