PipeIT2: Somatic Variant Calling Workflow for Ion Torrent Sequencing Data

Andrea Garofoli; Désirée Schnidrig; Charlotte K Y Ng

doi:10.1007/978-1-0716-2293-3_12

PipeIT2: Somatic Variant Calling Workflow for Ion Torrent Sequencing Data

Methods Mol Biol. 2022:2493:195-204. doi: 10.1007/978-1-0716-2293-3_12.

Authors

Andrea Garofoli¹, Désirée Schnidrig^{2

3}, Charlotte K Y Ng^{4

5}

Affiliations

¹ Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland.
² Department for BioMedical Research, University of Bern, Bern, Switzerland.
³ SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.
⁴ Department for BioMedical Research, University of Bern, Bern, Switzerland. [email protected].
⁵ SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland. [email protected].

PMID: 35751816
DOI: 10.1007/978-1-0716-2293-3_12

Abstract

The detection of somatic genetic variants forms the cornerstone of precision oncology. Molecular diagnostics laboratories require economical and rapid protocols to generate accurate variant calls for clinical purposes. The Ion Torrent sequencing platform is frequently used but lacks robust analysis workflows tailored to the needs of custom sequencing panels. We present PipeIT2, a somatic variant calling workflow for both matched tumor-germline and tumor-only analyses. PipeIT2 is enclosed in a Singularity container to ensure reproducibility and ease of deployment.

Keywords: Ion Torrent; Singularity; Somatic mutations; Tumor-only variant calling; Variant calling.

MeSH terms

High-Throughput Nucleotide Sequencing / methods
Humans
Neoplasms* / diagnosis
Neoplasms* / genetics
Precision Medicine
Reproducibility of Results
Workflow