Hello, I´m a newbie in bioinformatics. I want to preform a dn/ds analysis on cancer genes. For an specif gene, let's say BRCA1 should I use only the information on the MAF file or should I analyse all the patients variants?.

PD Papers such as:paper 1 paper 2 perform a dn/ds analysis on cancer genes, but the methods they use for obtaining the sequences are unclear as far as I could decipher

Thanks in advance