Garofoli, Andrea; Schnidrig, Désirée; Ng, Charlotte K Y (2022). PipeIT2: Somatic Variant Calling Workflow for Ion Torrent Sequencing Data. Methods in molecular biology, 2493, pp. 195-204. Springer 10.1007/978-1-0716-2293-3_12
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Garofoli2022_Protocol_PipeIT2SomaticVariantCallingWo.pdf - Published Version Restricted to registered users only Available under License Publisher holds Copyright. Author holds Copyright Download (222kB) | Request a copy |
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.
Item Type: |
Journal Article (Original Article) |
|---|---|
Division/Institute: |
04 Faculty of Medicine > Pre-clinic Human Medicine > BioMedical Research (DBMR) |
UniBE Contributor: |
Schnidrig, Désirée, Ng, Kiu Yan Charlotte |
Subjects: |
600 Technology > 610 Medicine & health |
ISSN: |
1940-6029 |
Publisher: |
Springer |
Language: |
English |
Submitter: |
Pubmed Import |
Date Deposited: |
27 Jun 2022 10:14 |
Last Modified: |
05 Dec 2022 16:21 |
Publisher DOI: |
10.1007/978-1-0716-2293-3_12 |
PubMed ID: |
35751816 |
Uncontrolled Keywords: |
Ion Torrent Singularity Somatic mutations Tumor-only variant calling Variant calling |
BORIS DOI: |
10.48350/170930 |
URI: |
https://boris.unibe.ch/id/eprint/170930 |
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