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

作者：Shin Sunguk; Lee Hanna; Son Hyeonju; Paik Soonmyung; Kim Sangwoo^*

来源：Bioinformatics, 2018, 34(7): 1232-1234.

DOI：10.1093/bioinformatics/btx719

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 similar to 98% reduction of false variants when combined to conventional public pipelines and similar to 48% to the in-house commercial solution, with a minimal loss of sensitivity.

• 出版日期2018-4-1