Identification of Somatic Variants in Cancer Genomes from Tissue and Liquid Biopsy Samples.

Somatic variant detection is an important step in the analysis of cancer genomes for basic research as well as precision oncology. Here, we review existing computational methods for identifying somatic mutations from tissue as well as liquid biopsy samples. We then describe steps to run VarNet (Krishnamachari et al., Nat Commun 13:4248, 2022), a variant caller using deep learning, to accurately identify single nucleotide variants (SNVs) and short insertion-deletion (indels) mutations from next-generation sequencing (NGS) of tumor tissue samples.