Fast and affordable benchtop sequencers (e.g. PGM from Ion Torrent) are becoming more important in improving personalized medical treatment. Still, distinguishing genetic variants between healthy and diseased individuals from sequencing errors remains a challenge
Here we present VARIFI, a pipeline for finding reliable genetic variants (SNPs and INDELs). We optimized parameters in VARIFI by analyzing more than 170 amplicon sequenced cancer samples produced on the PGM. In contrast to existing pipelines, VARIFI combines different analysis methods and, based on their concordance, assigns a confidence score to every identified variant. Furthermore, VARIFI applies variant filters for biases associated with the sequencing technologies (e.g. incorrectly called homopolymer-associated indels with Ion Torrent). VARIFI automatically extracts variant information from publicly available databases and incorporates methods for variant effect prediction.
VARIFI requires only little computational experience and no in-house compute power since the analyses are done on our server. Please read TUTORIAL for the instructions on how to use VARIFI and interpret its results.