Hi, I am looking for tools to identify somatic mutations (SNPs, CNVs, indels, etc) from a tumour sample (RNA-seq) which has been aligned with the human reference genome using STAR. I noticed that there are many tools (MuTect, MuSE, VarDict, etc) for generating a vcf file. It looks like these tools require both reference mutations from dbSNP/COSMIC, and the aligned file for normal sample. On the other hand, samtools mpileup converts BAM to VCF without these requirements. So, is it recommended to go ahead with samtools or use the other tools?
Meanwhile, I am reading research papers about the use of Machine/Deep Learning Techniques for the identification of mutations. Is there any way I can incorporate these techniques into my analysis?
Thanks in advance.