CellCoal: NGS simulation of single-cell somatic evolution

Posted on January 23, 2020 by dposada

Check my new simulator CellCoal for the coalescent simulation of single-cell sequencing genotypes. CellCoal simulates the history of single-cell samples obtained from somatic cell populations with different demographic histories and produces single-nucleotide variants under a variety of mutation models, sequencing read counts, and genotype likelihoods, considering allelic imbalance, allelic dropout, amplification, and sequencing errors, typical of this type of data.

Publication: https://academic.oup.com/mbe/article/37/5/1535/5728646

Code: https://github.com/dapogon/cellcoal

Manual: https://dapogon.github.io/cellcoal/cellcoal.manual.v1.1.html

 

Effect of sequencing coverage heterogeneity on single-cell genotypes. (A) Probability that the maximum likelihood genotype is wrong. (B) Proportion of genotypes called. (C) Total number of single-nucleotide variants (SNVs) called. GATK and true (GATK+ADO) are the likelihood models used for calling genotypes. Coverage dispersion corresponds to the negative binomial dispersion parameter. The smaller this parameter is, the more heterogeneity there is. At the top, 1×, 5×, and 25× are different overall sequencing depths. In the boxplots, the central line indicates the median, whereas the box limits correspond to the Q1 and Q3 quartiles and the asterisk to the mean.

 

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