Hi all! I have 4 pairs of matched tumor/normal exome sequencing experiments. These are from 4 patients with the same type of tumor. I want to detect tumor-specific somatic mutations.
Looking at the documentation of SomaticSniper, VarScan, GATK somaticIndelDetector and other tools, it seems they all can only process one pair (one patient) at a time. I was just thinking if there is some tool capable of performing multi-sample analysis - utilizing the information from all the patients and reporting tumor-specific variants. I can always process these 4 pairs separately and then compare the results myself, but if some tool could use its statistic model to process multiple samples directly, I would like to try it. Do you have any suggestions? Thanks.