webGQT: A Shiny Server for Genotype Query Tools for Model-Based Variant Filtering
SummaryGenotype Query Tools (GQT) were developed to discover disease-causing variations from billions of genotypes and millions of genomes, processes data at substantially higher speed over other existing methods. While GQT has been available to a wide audience as command-line software, the difficul...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2020-03-01
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| Series: | Frontiers in Genetics |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/article/10.3389/fgene.2020.00152/full |
| _version_ | 1811269603179888640 |
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| author | Meharji Arumilli Meharji Arumilli Ryan M. Layer Ryan M. Layer Marjo K. Hytönen Marjo K. Hytönen Hannes Lohi Hannes Lohi |
| author_facet | Meharji Arumilli Meharji Arumilli Ryan M. Layer Ryan M. Layer Marjo K. Hytönen Marjo K. Hytönen Hannes Lohi Hannes Lohi |
| author_sort | Meharji Arumilli |
| collection | DOAJ |
| description | SummaryGenotype Query Tools (GQT) were developed to discover disease-causing variations from billions of genotypes and millions of genomes, processes data at substantially higher speed over other existing methods. While GQT has been available to a wide audience as command-line software, the difficulty of constructing queries among non-IT or non-bioinformatics researchers has limited its applicability. To overcome this limitation, we developed webGQT, an easy-to-use tool with a graphical user interface. With pre-built queries across three modules, webGQT allows for pedigree analysis, case-control studies, and population frequency studies. As a package, webGQT allows researchers with less or no applied bioinformatics/IT experience to mine potential disease-causing variants from billions.ResultswebGQT offers a flexible and easy-to-use interface for model-based candidate variant filtering for Mendelian diseases from thousands to millions of genomes at a reduced computation time. Additionally, webGQT provides adjustable parameters to reduce false positives and rescue missing genotypes across all modules. Using a case study, we demonstrate the applicability of webGQT to query non-human genomes. In addition, we demonstrate the scalability of webGQT on large data sets by implementing complex population-specific queries on the 1000 Genomes Project Phase 3 data set, which includes 8.4 billion variants from 2504 individuals across 26 different populations. Furthermore, webGQT supports filtering single-nucleotide variants, short insertions/deletions, copy number or any other variant genotypes supported by the VCF specification. Our results show that webGQT can be used as an online web service, or deployed on personal computers or local servers within research groups.AvailabilitywebGQT is made available to the users in three forms: 1) as a webserver available at https://vm1138.kaj.pouta.csc.fi/webgqt/, 2) as an R package to install on personal computers, and 3) as part of the same R package to configure on the user's own servers. The application is available for installation at https://github.com/arumds/webgqt. |
| first_indexed | 2024-04-12T21:46:08Z |
| format | Article |
| id | doaj.art-0829a93d0b7d45f7b49c66bf83729ef4 |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-04-12T21:46:08Z |
| publishDate | 2020-03-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-0829a93d0b7d45f7b49c66bf83729ef42022-12-22T03:15:38ZengFrontiers Media S.A.Frontiers in Genetics1664-80212020-03-011110.3389/fgene.2020.00152496352webGQT: A Shiny Server for Genotype Query Tools for Model-Based Variant FilteringMeharji Arumilli0Meharji Arumilli1Ryan M. Layer2Ryan M. Layer3Marjo K. Hytönen4Marjo K. Hytönen5Hannes Lohi6Hannes Lohi7Department of Veterinary Biosciences, Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, FinlandGenetics Research Program, The Folkhälsan Research Center, Helsinki, FinlandDepartment of Computer Science, University of Colorado, Boulder, CO, United StatesThe BioFrontiers Institute, University of Colorado, Boulder, CO, United StatesDepartment of Veterinary Biosciences, Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, FinlandGenetics Research Program, The Folkhälsan Research Center, Helsinki, FinlandDepartment of Veterinary Biosciences, Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, FinlandGenetics Research Program, The Folkhälsan Research Center, Helsinki, FinlandSummaryGenotype Query Tools (GQT) were developed to discover disease-causing variations from billions of genotypes and millions of genomes, processes data at substantially higher speed over other existing methods. While GQT has been available to a wide audience as command-line software, the difficulty of constructing queries among non-IT or non-bioinformatics researchers has limited its applicability. To overcome this limitation, we developed webGQT, an easy-to-use tool with a graphical user interface. With pre-built queries across three modules, webGQT allows for pedigree analysis, case-control studies, and population frequency studies. As a package, webGQT allows researchers with less or no applied bioinformatics/IT experience to mine potential disease-causing variants from billions.ResultswebGQT offers a flexible and easy-to-use interface for model-based candidate variant filtering for Mendelian diseases from thousands to millions of genomes at a reduced computation time. Additionally, webGQT provides adjustable parameters to reduce false positives and rescue missing genotypes across all modules. Using a case study, we demonstrate the applicability of webGQT to query non-human genomes. In addition, we demonstrate the scalability of webGQT on large data sets by implementing complex population-specific queries on the 1000 Genomes Project Phase 3 data set, which includes 8.4 billion variants from 2504 individuals across 26 different populations. Furthermore, webGQT supports filtering single-nucleotide variants, short insertions/deletions, copy number or any other variant genotypes supported by the VCF specification. Our results show that webGQT can be used as an online web service, or deployed on personal computers or local servers within research groups.AvailabilitywebGQT is made available to the users in three forms: 1) as a webserver available at https://vm1138.kaj.pouta.csc.fi/webgqt/, 2) as an R package to install on personal computers, and 3) as part of the same R package to configure on the user's own servers. The application is available for installation at https://github.com/arumds/webgqt.https://www.frontiersin.org/article/10.3389/fgene.2020.00152/fullvariantfilteringR packageshiny serverGQTwebGQT |
| spellingShingle | Meharji Arumilli Meharji Arumilli Ryan M. Layer Ryan M. Layer Marjo K. Hytönen Marjo K. Hytönen Hannes Lohi Hannes Lohi webGQT: A Shiny Server for Genotype Query Tools for Model-Based Variant Filtering Frontiers in Genetics variant filtering R package shiny server GQT webGQT |
| title | webGQT: A Shiny Server for Genotype Query Tools for Model-Based Variant Filtering |
| title_full | webGQT: A Shiny Server for Genotype Query Tools for Model-Based Variant Filtering |
| title_fullStr | webGQT: A Shiny Server for Genotype Query Tools for Model-Based Variant Filtering |
| title_full_unstemmed | webGQT: A Shiny Server for Genotype Query Tools for Model-Based Variant Filtering |
| title_short | webGQT: A Shiny Server for Genotype Query Tools for Model-Based Variant Filtering |
| title_sort | webgqt a shiny server for genotype query tools for model based variant filtering |
| topic | variant filtering R package shiny server GQT webGQT |
| url | https://www.frontiersin.org/article/10.3389/fgene.2020.00152/full |
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