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Distinguishing somatic structural variants (SVs) from germline SVs in the absence of matched normal samples has significant value in elucidating disease-driving processes in cancer. Here, we present a protocol for classifying germline SVs in tumor-only contexts using a support vector machine (SVM)-based algorithm. We describe steps for preparing input data and identifying SVs from whole-genome sequencing (WGS) of tumor samples using the SV caller SvABA. We then detail classification procedures via our germline and tumor structural variant classifier (GaTSV). For complete details on the use and execution of this protocol, please refer to Chukwu et al..