Darby, C. A., Fitch, J. R., Brennan, P. J., Kelly, B. J., Bir, N., Magrini, V., Leonard, J., Cottrell, C. E., Gastier-Foster, J. M., Wilson, R. K., Mardis, E. R., White, P., Langmead, B., Schatz, M. C. (August 2019) Samovar: Single-Sample Mosaic Single-Nucleotide Variant Calling with Linked Reads. iScience, 18 (Specia). pp. 1-10. ISSN 2589-0042 (Public Dataset)
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Abstract
Linked-read sequencing enables greatly improves haplotype assembly over standard paired-end analysis. The detection of mosaic single-nucleotide variants benefits from haplotype assembly when the model is informed by the mapping between constituent reads and linked reads. Samovar evaluates haplotype-discordant reads identified through linked-read sequencing, thus enabling phasing and mosaic variant detection across the entire genome. Samovar trains a random forest model to score candidate sites using a dataset that considers read quality, phasing, and linked-read characteristics. Samovar calls mosaic single-nucleotide variants (SNVs) within a single sample with accuracy comparable with what previously required trios or matched tumor/normal pairs and outperforms single-sample mosaic variant callers at minor allele frequency 5%-50% with at least 30X coverage. Samovar finds somatic variants in both tumor and normal whole-genome sequencing from 13 pediatric cancer cases that can be corroborated with high recall with whole exome sequencing. Samovar is available open-source at https://github.com/cdarby/samovar under the MIT license.
| Item Type: | Paper |
|---|---|
| Subjects: | bioinformatics > genomics and proteomics bioinformatics > genomics and proteomics > annotation > variant calling |
| CSHL Authors: | |
| Communities: | CSHL labs > Schatz lab |
| Depositing User: | Matthew Dunn |
| Date: | 30 August 2019 |
| Date Deposited: | 29 Jul 2019 15:14 |
| Last Modified: | 29 Jun 2021 19:11 |
| PMCID: | PMC6609817 |
| Related URLs: | |
| Dataset ID: |
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| URI: | https://repository.cshl.edu/id/eprint/38144 |
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