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Genome Biol. 2019 Apr 1;20(1):68. doi: 10.1186/s13059-019-1673-8.

Conbase: a software for unsupervised discovery of clonal somatic mutations in single cells through read phasing.

Author information

1
Department of Cell and Molecular Biology, Karolinska Institutet, Solna, Sweden. joanna.hard@ki.se.
2
Department of Cell and Molecular Biology, Karolinska Institutet, Solna, Sweden.
3
Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Scilifelab, Uppsala University, Uppsala, Sweden.
4
Division of Gene Technology, Scilifelab, KTH Royal Institute of Technology, Solna, Sweden.
5
Center for Infectious Medicine, Department of Medicine, Karolinska Institutet, Huddinge, Sweden.
6
Department of Cell and Molecular Biology, Karolinska Institutet, Solna, Sweden. jonas.frisen@ki.se.

Abstract

Accurate variant calling and genotyping represent major limiting factors for downstream applications of single-cell genomics. Here, we report Conbase for the identification of somatic mutations in single-cell DNA sequencing data. Conbase leverages phased read data from multiple samples in a dataset to achieve increased confidence in somatic variant calls and genotype predictions. Comparing the performance of Conbase to three other methods, we find that Conbase performs best in terms of false discovery rate and specificity and provides superior robustness on simulated data, in vitro expanded fibroblasts and clonal lymphocyte populations isolated directly from a healthy human donor.

KEYWORDS:

Single-cell DNA sequencing; Single-cell variant calling; Somatic variation

PMID:
30935387
PMCID:
PMC6444814
DOI:
10.1186/s13059-019-1673-8
[Indexed for MEDLINE]
Free PMC Article

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