A presentation about variant tools (Oct, 19, 2011), updated for version 1.0

News

  • May 16, 2013: Release of variant tools 1.0.6, which contains a lot of small features and bug fixes.
  • Mar 20, 2013: Release of variant tools 1.0.5. This release adds commands vtools admin --update_resource and vtools_report sequences, and allows the use of arbitrary characters for names of variant tables.
  • Feb 20, 2013: Release of variant tools 1.0.4. This release comes with numerous bug fixed and new minor features. Please check the ChangeLog for details.
  • Oct 21, Nov 10, Nov 26, and Nov 29. 2012: Release of variant tools 1.0.3a, b, c and d to address various small issues.
  • Sep 25, 2012: Release of variant tools version 1.0.3, with new features and improvements in vtools associate, vtools update, vtools phenotype and vtools_report commands.
  • Jul 9th, 2012: Release of variant tools version 1.0.3rc1. Other than a few bug fixes and major performance improvements, this release introduces new commands vtools associate and vtools admin, with more than 20 association tests implemented under a unified association test framework.
  • Jan 24th, 2012: Release of variant tools version 1.0.2. This release fixes a major bug that causes duplicate output in commands vtools output and vtools export when range-based annotation databases are used. All users are recommended to upgrade.
  • more ...
  • Jan 2nd, 2012: Release of variant tools version 1.0.1. This version contains a few new features and bug fixes, and more importantly, dramatic performance improvement for many commands. Please refer to ChangeLog for details about this release.
  • Dec 30th, 2011: the gwasCatalog annotation source is available for download. See examples of how to use gwasCatalog to find published GWA hits that are near your variants.
  • Dec 15th, 2011: Two new annotation sources are available: Cancer Gene Census from the Cancer Genome Project, and the 5400 exomes EVS annotation database from the NHLBI Exome Sequencing Project.
  • Dec 4th, 2011: An application note that describes variant tools has been published online in Bioinformatics.
  • Nov 13, 2011: Release of variant tools version 1.0.
  • Jan 24th, 2012: Release of variant tools version 1.0.2. This release fixes a major bug that causes duplicate output in commands vtools output and vtools export when range-based annotation databases are used. All users are recommended to upgrade.
  • Jan 2nd, 2012: Release of variant tools version 1.0.1. This version contains a few new features and bug fixes, and more importantly, dramatic performance improvement for many commands. Please refer to ChangeLog for details about this release.
  • Dec 30th, 2011: the gwasCatalog annotation source is available for download. See examples of how to use gwasCatalog to find published GWA hits that are near your variants.
  • Dec 15th, 2011: Two new annotation sources are available: Cancer Gene Census from the Cancer Genome Project, and the 5400 exomes EVS annotation database from the NHLBI Exome Sequencing Project.
  • Dec 4th, 2011: An application note that describes variant tools has been published online in Bioinformatics.
  • Nov 13, 2011: Release of variant tools version 1.0.
  • Nov 7, 2011: A new annotation source called EVS (Exome Variant Server) is available consisting of exome sequencing variants from the NHLBI Exome Sequencing Project (ESP). This data was retrieved from the project's EVS server and contains population-specific allele frequencies (currently for European Americans and African Americans) and various functional annotations for predicted variants in approximately 2500 exomes.
  • Nov 2, 2011: Release of release candidate version 1.0rc3. This version adds option --jobs to a number of vtools commands and allow them to execute in multiple threads or processes. User interface is further cleaned for the final 1.0 release. As a result, support for the MySQL backend is temporarily disabled.
  • Oct 16, 2011: Release of release candidate version 1.0rc2. This version has a new option --children for command vtools init, which allows the creation of a project by merging multiple subprojects.
  • Oct 7, 2011: Release of release candidate version 1.0rc1. This version has a new vtools export command that can export in ANNOVAR and VCF formats.
  • Sep 27, 2011: Release of the second beta. This version contains full Python 3 support and a much more powerful vtools import command.
  • Sep 10, 2011: Release of 1.0 beta.
  • July 15, 2011: Initial public release.

Overview

variant tools is a software tool for the annotation, selection, and analysis of variants in the context of next-gen sequencing analysis. Unlike some other tools used for Next-Gen sequencing analysis, variant tools is project based and provide a whole set of tools to manipulate and analyze genetic variants. Using this tool, you can

  • Import samples (genetic variants and phenotypes) or lists of variants from source files in vcf and other formats.
  • Link the project to multiple annotation sources to annotate variants, even if the annotation source does not use the same reference genome as your input data.
  • Display, output, or export variants with their annotations.
  • Get summary statistics of variants and phenotype at sample and variant level, for all or part of the samples.
  • Remove samples or variant tools under certain conditions.
  • Select variants according to one or more conditions based on sample property, and annotation.
  • Compare lists of selected variants.
  • Export samples with selected variants in other formats to be analyzed by other programs.
  • Analyze selected variants using one or more association tests.
  • Select variants according to association test results.
  • ...

In summary, variant tools provides an environment for integrated annotation and analysis of genetic variants. Please refer to a list of tutorials to get started.

Major features

The development of variant tools was motivated by the fact that, although there are many annotation sources, it is not easy to apply them to real-world next-gen sequencing analysis (while also keeping track of which variants were detected in which samples). In addition, although a large number of association tests have been proposed, implementations of these methods vary in input and output formats, and their ability to handle real world datasets. To simplify such analysis, variant tools

  • Supports a large number of import/export formats, and allows you to track the sample from which variants are imported. For example, the following commands import data from two different platforms, and create separate variant tables for them.
  • Supports a primary and an alternative reference genome through the use of the USCS liftover tool. For example, variants can be inputted in hg18, and be annotated using databases for the hg19 reference genome. You can even import data that use different reference genomes into the same project.
  • Efficient and simple use of fields to annotate and select variants. Fields from different sources for different variant tables can be summarized and used as if they are from a single large table that contains all variants and fields. Because all fields are readily available, selection of variants is extremely fast compared to other applications.
  • Calculate sample and genotype statistics and use them to select and annotate variants.
  • Provide an unified framework and interface for more than 20 association tests.
  • Highly optimized and use multiple processes to efficiently handle large-scale whole-genome or exome studies.

Citation for variant tools

Please cite

F. Anthony San Lucas, Gao Wang, Paul Scheet, and Bo Peng (2012) Integrated annotation and analysis of genetic variants from next-generation sequencing studies with variant tools, Bioinformatics 28 (3): 421-422.

if you find variant tools helpful and use it in your publication. Thank you.