PipeIT2: Somatic Variant Calling Workflow for Ion Torrent Sequencing Data.

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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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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