Tool:OakVar: genomic variant analysis tool

Question

[Ryangguk Kim]

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:

• GitHub: https://github.com/rkimoakbioinformatics/oakvar
• Documentation: https://oakvar.readthedocs.io
• PyPI: https://pypi.org/project/oakvar

Answer 1

[Ryangguk Kim]

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.