Variant calling, the detection of SNPs and INDELs, plays a particularly important role in Ion Torrent data due to its propensity for homopolymer errors.  It’s particularly challenging to sort the insertions and deletions that occur through sequencing errors from true differences from the reference sequence.  A variant calling plugin is included in the Ion Torrent analysis pipeline that assists in the identification of SNPs and INDELs.  Utilizing SAMtools the plugin produces a variant sample report using settings adjusted to match the error model in Ion Torrent data.  Using recently sequenced E. coli DH10B data from a 316 chip and an artificially mutated E. coli genome the variant analysis plugin settings were compared to other samtools settings to try to find settings that produce the most true variants while avoiding false positives.  This mutated genome and a genome comprised of only homopolymer errors were also used to compare Illumina’s MiSeq technology to Ion Torrent in terms of variant analysis.