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 xe2x88xbc98% reduction of false variants when combined to conventional public pipelines and xe2x88xbc48% to the in-house commercial solution, with a minimal loss of sensitivity.