Hi! I am new to cancer genome. I would like to apply maftools to analysis MAF files. The required input files: (1) an MAF file - can be gz compressed. Required. (2) an optional but recommended clinical data associated with each sample/Tumor_Sample_Barcode in MAF. (3) an optional copy number data if available. Can be GISTIC output or a custom table containing sample names, gene names and copy-number status (Amp or Del). Before processing with maftools, we need to merge MAFs from all samples into a single MAF. My questions are (a). how to merge multiple MAF files into a single MAF file. (b) How to create sample/Tumor_Sample_Barcode in MAF?
I would appreciate if someone can guide me to conduct significant somatic mutation variants analysis. Many thanks!