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Updated: Jun 4, 2025

Detecting Somatic Genetic Alterations in Tumor Specimens by Exon Capture and Massively Parallel Sequencing
Published on: October 18, 2013
Protocol for the assessment, improvement, and harmonization of somatic variant calling using ONCOLINER
Rodrigo Martín1, Nicolás Gaitán1, David Torrents2
1Life Sciences Department, Barcelona Supercomputing Center (BSC), Barcelona, Spain.
None:
The interoperability of variant identification pipelines is fundamental for achieving consistent clinical care across oncology research centers and hospitals. Here, we present a protocol for using ONCOLINER, a platform for the assessment, improvement, and harmonization of somatic variant discovery of multiple pipelines. We describe steps for acquiring benchmarking datasets and executing the user variant calling pipeline. We then detail the procedures for performing analyses to produce user-friendly reports showing the quality, scope, and applicable improvements for each tumor genome analysis. For complete details on the use and execution of this protocol, please refer to Martín et al.1.
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