  With recent advances in sequencing technology it has become affordable and
practical to sequence genomes to very high depth-of-coverage, allowing
researchers to discover low-frequency variants in the genome. However, due to
the errors in sequencing it is an active area of research to develop algorithms
that can separate noise from the true variants. LoFreq is a state of the art
algorithm for low-frequency variant detection but has a relatively long runtime
compared to other tools. In addition to this, the interface for running in
parallel could be simplified, allowing for multithreading as well as
distributing jobs to a cluster. In this work we describe some specific
contributions to LoFreq that remedy these issues.
