Bahonar S, Montazeri H. Somatic Single-Nucleotide Variant Calling from Single-Cell DNA Sequencing Data Using SCAN-SNV.
Methods Mol Biol 2022;
2493:267-277. [PMID:
35751821 DOI:
10.1007/978-1-0716-2293-3_17]
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Abstract
SCAN-SNV is a recent computational tool for somatic single-nucleotide variant (SNV) identification from the single-cell DNA sequencing data. The workflow of the SCAN-SNV package is as follows. First, candidate somatic SNVs and credible heterozygous single-nucleotide polymorphisms (hSNP) are obtained by analyzing single-cell and matched bulk sequencing data, respectively. Subsequently, SCAN-SNV estimates genome-wide allele-specific amplification balance (AB) at any position of DNA sequencing data using a probabilistic spatial statistical model. Finally, candidate somatic SNVs that are likely artifacts according to the AB predictions are further removed to obtain putative mutations. This chapter provides a step-by-step practical guide of the package by explaining how to install and use the variance caller in a real-world example.
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