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