Eddie K K Ip1,2, Clinton Hadinata1, Joshua W K Ho1,2,3, Eleni Giannoulatou1,2. 1. Victor Chang Cardiac Research Institute, Sydney, Australia. 2. St. Vincent's Clinical School, UNSW Sydney, Sydney, Australia. 3. School of Biomedical Sciences, The University of Hong Kong, Hong Kong, China.
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.
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.
Authors: Hien Thi Thu Le; Linh Nhat Nguyen; Hang Le Bich Pham; Hao Thi My Le; Toan Duc Luong; Hue Thi Thu Huynh; Van Tuong Nguyen; Hai Van Nong; Irene Teixidor-Toneu; Hugo J De Boer; Vincent Manzanilla Journal: Front Plant Sci Date: 2022-07-13 Impact factor: 6.627