I want to analyze the variation status of some genes in some cancer, And for this purpose want to use the ICGC data (there is a large number of patients). Now I have two choices :
- Downloading the VCF files of patients and analyze them.
- Downloading the BAM file of my interest gene position and create the VCF file, then analyze them.
According to my purpose, which option is more recommended and accepted?
Thanks for any help