Methods Mol Biol. 2022;2493:267-277. doi: 10.1007/978-1-0716-2293-3_17.
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.
PMID:35751821 | DOI:10.1007/978-1-0716-2293-3_17
