Does anyone know of an acceptable workflow/pipeline for processing cancer exome data without a matched normal? I understand that without the normal, we won't be able to distinguish between germline and somatic mutations with 100% certainty. Even so, I would like to process our data. I have already prepped my data using the steps outlined GATK best practices (align, sort, remove dups, index, indel realign, base recalibration). What is the next step (software, analysis, etc)?
Thanks for your help!