Bioinformatics. 2018 Apr 01;34(7):1232-1234. doi: 10.1093/bioinformatics/btx719.

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

Bioinformatics (Oxford, England)

Sunguk Shin, Hanna Lee, Hyeonju Son, Soonmyung Paik, Sangwoo Kim

PMID: 29126106 DOI: 10.1093/bioinformatics/btx719

Abstract

SUMMARY: 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.

AVAILABILITY AND IMPLEMENTATION: The program with a detailed manual is available at https://sourceforge.net/projects/airvf/.

CONTACT: [email protected].

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

MeSH terms

• Diagnostic Errors*
• Gene Frequency
• High-Throughput Nucleotide Sequencing / methods
• Humans
• Sensitivity and Specificity
• Software*

Publication Types

• Journal Article
• Research Support, Non-U.S. Gov't