AIRVF: a filtering toolbox for precise variant calling in Ion Torrent sequencing

Ion Torrent sequencing is one of the most frequently used platforms in healthcare research and industry. Despite many advantages, platform-specific artifacts complicate efficient separation of true variants from errors, especially in variants with lower allele frequencies (<15%). Here, we developed a multi-step filtering toolbox AIRVF that works on flowgram, raw and mapped reads and called variants to reduce artifact-driven false variant calls. Tests on sequencing data of standard reference material showed up to ∼98% reduction of false variants when combined to conventional public pipelines and ∼48% to the in-house commercial solution, with a minimal loss of sensitivity. The program with a detailed manual is available at https://sourceforge.net/projects/airvf/. swkim@yuhs.ac Supplementary data are available at Bioinformatics online.