Nyuk Hien Wong Received: In the actual era of smart homes and smart grids, advanced technological systems that allow the automation of domestic tasks are developing rapidly. There are numerous technologies and applications that can be installed in smart homes today.
Advanced Search Abstract Summary: TrioVis is a visual analytics tool developed for filtering on coverage and variant frequency for genomic variants from exome sequencing of parent—child trios. In TrioVis, the variant data are organized by grouping each variant based on the laws of Mendelian inheritance.
Taking three Variant Call Format files as input, TrioVis allows the user to test different coverage thresholds i. Executables, source code and sample data are available at https: Screencast is available at http: Analysis of parent—child trios is one of the strategies for identifying single pathogenic mutations among the thousands to millions of genomic variants.
By sequencing, the patient as well as his or her parents, variants can be filtered based on consistency or inconsistency according to the laws of Mendelian inheritance. Although filtering based on inheritance pattern seems to be straight-forward, distinguishing true variation from artefacts and false negatives while retaining sensitivity is a challenging task because of the sequencing error rate and the interdependency of sequencing quality for multiple samples.
A previous study Bamshad et al. One of the metrics commonly used to filter variants is the depth of coverage. Researchers we interviewed adjust the coverage threshold based on the overall coverage and their intuition without any visual aids.
The optimal coverage thresholds also depend on other factors, such as the suspected type of mutation, whether somatic or inherited, and the stringency of analysis.
Although finding the optimal coverage threshold can be automated to some extent, it still requires fine adjustments of the filtering setting for variant discovery. We present a visual analytics tool, TrioVis, designed to help the analytical reasoning process of setting coverage thresholds to filter variants from parent—child trio sequencing experiments.
It visualizes variants in a structured table and provides interactive visual interfaces to let the researcher dynamically and interactively test different threshold settings and change levels of stringency.
Based on these read counts, variant frequencies for each variant are calculated. The user interface consists of five sections: Each section focuses on a specific aspect of trio data and offers specific interactive features to calibrate the thresholds.
Father, mother and child are colour-coded in green, orange and blue, respectively. A The main table. B The global variant count bar graphs. C The variant frequency sliders. D The coverage sliders. E The histogram view showing the father sample Fig.
E The histogram view showing the father sample The main table Fig. Each block consists of three histograms, conveying the distribution of variants based on the read depth per sample.
The background colour of each block is determined by whether it is consistent white or inconsistent grey with the laws of Mendelian inheritance. The global variant count bar graphs Fig.
By changing coverage settings, the researcher aims to minimize the number of inconsistent calls while keeping the number of consistent calls high. The variant frequency sliders Fig.
These sliders can be used by the researchers to adjust the ranges for variant frequency for genotyping variants for that sample. The coverage sliders Fig. These sliders also represent the distribution of variants based on coverage values. Finally, the histogram view Fig.
Hovering the mouse over the stacked bar graph highlights cells in the main table, showing where these variants are represented. This view aids the researcher to calibrate the coverage threshold for the selected sample. The variant data can be investigated under two assumptions: The researcher can also select specific blocks to export variants of a specific inheritance pattern i.
By visualizing variants in a novel table layout based on the inheritance laws, it allows the researcher to gain insights into the global effect of filtering in the context of trio analysis.
The researcher can export the filtered result as VCF files for subsequent analysis to annotate variants to genes, using annotation tools, such as Annotate-It Sifrim et al.The Library of Congress > Chronicling America > The Big Sandy news.
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