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- Title
dv-trio: a family-based variant calling pipeline using DeepVariant.
- Authors
Ip, Eddie K K; Hadinata, Clinton; Ho, Joshua W K; Giannoulatou, Eleni
- Abstract
Motivation In 2018, Google published an innovative variant caller, DeepVariant, which converts pileups of sequence reads into images and uses a deep neural network to identify single-nucleotide variants and small insertion/deletions from next-generation sequencing data. This approach outperforms existing state-of-the-art tools. However, DeepVariant was designed to call variants within a single sample. In disease sequencing studies, the ability to examine a family trio (father-mother-affected child) provides greater power for disease mutation discovery. Results To further improve DeepVariant's variant calling accuracy in family-based sequencing studies, we have developed a family-based variant calling pipeline, dv-trio, which incorporates the trio information from the Mendelian genetic model into variant calling based on DeepVariant. Availability and implementation dv-trio is available via an open source BSD3 license at GitHub (https://github.com/VCCRI/dv-trio/). Contact e.giannoulatou@victorchang.edu.au Supplementary information Supplementary data are available at Bioinformatics online.
- Subjects
GOOGLE Inc.; PIPELINES; GENETIC models; NUCLEOTIDE sequencing; PIPELINE inspection; FATHERS
- Publication
Bioinformatics, 2020, Vol 36, Issue 11, p3549
- ISSN
1367-4803
- Publication type
Article
- DOI
10.1093/bioinformatics/btaa116