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GATK Analysis Parameters
Hi! I am new to next gen sequencing and started working with Ion Torrent's PGM for the Targeted Gene Sequencing using the AmpliSeq Custom Panel. I need to get the analysis going and asking for help from others. I have been reading a lot and have a better understanding of the workflow but not having bioinformatics background has been difficult to run the GATK in our Linux system. Can anyone help me with analysis parameters? Or anywhere I can find them? I have 175 patients and 31 genes in my panel.