This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Tool: OakVar: genomic variant analysis tool

OakVar is a genomic variant analysis platform. You can

  • Annotate genomic variants with diverse annotation sources.
  • Make databases of annotated variants.
  • Query annotated variants with filter sets.
  • Make reports in diverse formats.
  • Visualize annotated variants with graphical user interface.
  • Works via CLI and GUI.

One main goal of OakVar is to become a platform on which developers can easily develop, run, and distribute CLI and GUI genomics apps.

OakVar is a fork of OpenCRAVAT and has new development directions. I was the lead architect of OpenCRAVAT, in which I am not involved anymore. OakVar is currently compatible with OpenCRAVAT modules and job files.

An R wrapper for OakVar exists, Roakvar. See Roakvar: do genomic variant analyses with R for its announcement.

Links:

genomics variant
• 1,616 views • link
updated by Ram Ram • written by Ryangguk Kim • Ryangguk Kim

1 answer

OakVar v2.4.5 has been released. This version has the following updates:

  • Line breaks in annotation results are correctly escaped with ov report. This fixes the issue at https://github.com/KarchinLab/open-cravat/issues/106.

  • CLI commands alignment among CLI, Python, and R. For example:

    CLI:

     >ov module ls

    Python:

     >import oakvar
 >oakvar.ov_module_ls()

    R:

     >devtools::install_github("rkimoakbioinformatics/roakvar")
 >library(roakvar)
 >roakvar::ov.module.ls()
  • Python subprocess calls to CLI functions such as oakvar.ov_module_ls() will return returncode 0 if no error was produced.
  • ov gui will print error messages to stdout if —debug option is given.
  • ov module install will automatically install PyPI dependencies defined in OakVar modules’ yml files with requires_pypi or pypi_dependency.- Improved the speed of handling configuration files.
  • Improved exception handling.
  • Fixed that the number of unique variants did not show on the job table of ov gui.
  • Fixed a bug in using —package option with ov run and ov report.
  • Refactored the mechanism for handling —package and --confpath options to ov run and ov report.
  • Refactored the handling of CLI command functions for better alignment among CLI, Python, and R.
  • Refactored the code so that no error nor warning is reported by pyright and pylance.
• 0 views • link
written by Ryangguk Kim • Ryangguk Kim

Log in to answer this question.

More posts like this