SCG specifications


Unique identifier OMICS_11814
Name SCG
Alternative name Single Cell Genotyper
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Cell-target matrix
Output data The input data is expected to be discrete observations of point mutations, usually SNVs, but other types of data can be used.
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Stability Stable
panda, numpy, scipy, PyYaml
Maintained Yes


No version available



  • person_outline Sohrab P. Shah

Publication for Single Cell Genotyper

SCG citations


Sensitivity to sequencing depth in single cell cancer genomics

Genome Med
PMCID: 5901877
PMID: 29661213
DOI: 10.1186/s13073-018-0537-2

[…] lt parameters. Sensitivity was evaluated by assessing the recall of the CNVs and segment breakpoints at the different sequencing depths.Clonal genotypes were estimated from the somatic SNVs using the Single-Cell Genotyper (SCG) [] (Additional file : Note), and their recall across sequencing depth was measured with the adjusted Rand Index [], a version of the Rand Index corrected for chance []. The […]


Current Progresses of Single Cell DNA Sequencing in Breast Cancer Research

PMCID: 5599901
PMID: 28924377
DOI: 10.7150/ijbs.19627

[…] clonal lineage tress from somatic SNVs of single cells, which accounts for genotyping errors and tests for unobserved subpopulations . Ginkon can construct phylogenetic trees of cells by using CNAs . Single Cell Genotyper (SCG) infers clonal genotype and population structure by inputting a cell-target matrix, which simultaneously addresses the technical noise in single cell data by taking doublets […]

SCG institution(s)
Department of Molecular Oncology, BC Cancer Agency, Vancouver, BC, Canada; Graduate Bioinformatics Training Program, University of British Columbia, Vancouver, BC, Canada; School of Computing Science, Simon Fraser University, Burnaby, BC, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada; Department of Gynecology and Obstetrics, University of British Columbia, Vancouver, BC, Canada; Department of Statistics, University of British Columbia, Vancouver, BC, Canada; Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, Canada
SCG funding source(s)
The BC Cancer Foundation; the Canadian Breast Cancer Foundation; the Canadian Cancer Society Research Institute (impact grant 701584); the Terry Fox Research Institute (PPG program on forme fruste tumors); Canadian Institutes for Health Research (CIHR) (grant MOP-115170); CIHR Foundation (grant FDN-143246); a CIHR new investigator grant (MSH-261515); a Charles Best CIHR doctoral scholarship; a Frederick Banting doctoral scholarship; Canada Research Chairs; a Michael Smith Foundation for Health Research scholar

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