I just wanted to discuss the reliability of the tool. I understand that it is a high performing variant caller but it seems that the tool was made for DNA-seq? Reason being, it uses BWA aligner as shown in this paper. However, it also uses mutation callers that work "well" for RNAseq variant calling (JointSNVMix2, Mutect, SomaticSniper).
I am also curious if using Mutect2 vcf files (which are in v4.2 format) rather than Mutect1 vcf files will cause any issues?
Again, just wanted to open up discussion to speak with any one with experience using SomaticSeq for RNAseq variant calling.
Thanks a lot for your time and help!