Controlled vs Public MAFs

Question

[Jn Rmro]

Hi everyone.

I would like to do a pan-TCGA analysis. I am currently downloading MAF files using the manifests and the gdc data transfer tool. I've noticed 3 different MAF files to use:

• mc3.v0.2.8.PUBLIC.maf.gz, from A, B
• mc3.v0.2.8.CONTROLLED.maf.gz, from A
• TCGA_consolidated.abs_mafs_truncated.fixed.txt.gz, from B

1. How does the public MAF file differ from the controlled MAF file?
2. What is the effect of running ABSOLUTE prior to MAF creation (getting more accurate results?)

Thanks.

A: https://gdc.cancer.gov/about-data/publications/mc3-2017

B: https://gdc.cancer.gov/about-data/publications/pancanatlas