I have started recently my adventure in the bioinformatic world. I have made some RNA-Seq analysis, as differential expression and Gene Set Enrichment Analysis, with the help of several pipelines available out there.
Right now I'm starting to analyse WES raw data from tumor and normal-adjacent tissue in order to find somatic mutations, although I'm facing some difficulties finding the most appropriate pipeline to do so. I know there's the GATK pipeline, as well as the GDC's. However, I'm wondering whether there's other complete and comprehensive pipelines, with information about software and command-line guidelines.
Thanks in advance.