| Autor: |
Charlotte A. Darby, James R. Fitch, Patrick J. Brennan, Benjamin J. Kelly, Natalie Bir, Vincent Magrini, Jeffrey Leonard, Catherine E. Cottrell, Julie M. Gastier-Foster, Richard K. Wilson, Elaine R. Mardis, Peter White, Ben Langmead, Michael C. Schatz |
| Jazyk: |
angličtina |
| Rok vydání: |
2019 |
| Předmět: |
|
| Zdroj: |
iScience, Vol 18, Iss , Pp 1-10 (2019) |
| Druh dokumentu: |
article |
| ISSN: |
2589-0042 |
| DOI: |
10.1016/j.isci.2019.05.037 |
| Popis: |
Summary: 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. : Biological Sciences; Genomics; Bioinformatics Subject Areas: Biological Sciences, Genomics, Bioinformatics |
| Databáze: |
Directory of Open Access Journals |
| Externí odkaz: |
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