Skip to contents

Numbat is a haplotype-aware CNV caller from single-cell and spatial transcriptomics data. It integrates signals from gene expression, allelic ratio, and population-derived haplotype information to accurately infer allele-specific CNVs in single cells and reconstruct their lineage relationship.

Numbat can be used to: 1. Detect allele-specific copy number variations from scRNA-seq and spatial transcriptomics 2. Differentiate tumor versus normal cells in the tumor microenvironment 3. Infer the clonal architecture and evolutionary history of profiled tumors.


Numbat does not require paired DNA or genotype data and operates solely on the donor scRNA-seq data (for example, 10x Cell Ranger output). For details of the method, please checkout our paper:

Teng Gao, Ruslan Soldatov, Hirak Sarkar, Adam Kurkiewicz, Evan Biederstedt, Po-Ru Loh, Peter Kharchenko. Haplotype-aware analysis of somatic copy number variations from single-cell transcriptomes. Nature Biotechnology (2022).

User Guide

For a complete guide, please see Numbat User Guide.


We appreciate your feedback! Please raise a github issue for bugs, questions and new feature requests. For bug reports, please attach full log, error message, input parameters, and ideally a reproducible example (if possible).