Next generation sequencing (NGS) is the core technology that has made high-throughput genetic and genomic studies possible, and in turn has greatly impacted the field of pharmacogenetics and pharmacogenomics. NGS is rapidly replacing many competing techniques and becoming mature enough for wide-spread research use in industry with many applications (e.g., RNA-Seq). The software and computational tools used in the analysis of such data are much more diverse (and arguably complex) than the sequencing techniques and wet bench protocols used to produce the data. With that diversity, there are many analysis "degrees of freedom" that underlie the statistical and bioinformatic workflow. At this roundtable, we will discuss what tools are being used and what steps have the greatest impact on the end result, based on empirical studies and user experience. More consensus in this area would improve the reliability, reproducibility, and confidence with which findings arising from NGS can used in discovery, development, and ultimately to support regulatory decision making.