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

Abstract

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.