Hi, I am running a cancer driver gene analysis with oncodrivefml. I am using a maf file from TCGA biolinks and a cohort-level maf file from GDC portal. For an elements file that is required as input for oncodriveFML command line tool, I used a default elements file provided by the repository (cds.tsv). I have warnings when I run the command line tool, saying "Background mismatch at position xxx at "GENE_NAME"" for a significant number of genes.
I tried running it with a web-based tool, but as the default build parameter for this is hg19, I moved to a command line tool. If anyone has an experience with running oncodrivefml on command-line, could you please help me with this issue or help me understand what this warning means? or if anyone can suggest an alternative cancer driver gene selection analysis tool for hg38, that would also be very helpful, thanks! I have results from dndscv and mutsigcv for now.
