Accurate single-cell genotyping utilizing information from the local genome territory

Single-nucleotide variant (SNV) detection in the genome of single cells is affected by DNA amplification artefacts, including imbalanced alleles and early PCR errors. Existing single-cell genotyper accuracy often depends on the quality and coordination of both the target single-cell and external data, such as heterozygous profiles determined by bulk data. In most single-cell studies, information from different sources is not perfectly matched. High-accuracy SNV detection with a limited single data source remains a challenge. We developed a new variant detection method, SCOUT (Single Cell Genotyper Utilizing Information from Local Genome Territory), the greatest advantage of which is not requiring external data while base calling. By leveraging base count information from the adjacent genomic region, SCOUT classifies all candidate SNVs into homozygous, heterozygous, intermediate and low major allele SNVs according to the highest likelihood score. Compared with other genotypers, SCOUT improves the variant detection performance by 2.0–77.5% in real and simulated single-cell datasets. Furthermore, the running time of SCOUT increases linearly with sequence length; as a result, it shows 400% average acceleration in operating efficiency compared with other methods.