Tool: open-cravat: variant annotation tool
gravatar for slcrick
6 months ago by
United States
slcrick120 wrote:

open-cravat is an open-source platform for rapidly developing, using, and disseminating variant annotation tools.

It can handle unlimited number of variants in VCF format input files as well as its own input format and produce tab-separated text output files and excel spreadsheets. It is command-line-based as well as GUI-based. Its web visualization tool gives interactive filtering and sorting and tables and "widgets" which are graphic components to show annotation results (network graphs and gene diagrams with your variants on, for example). It is written in Python and installed with a pip install and has its own module manager.

It is modular and open-source, and it is easy to write input and output format converters and custom report generators as well as custom annotators and gene mappers. You write only minimum parts specific to your module since heavy lifting is done by open-cravat. You can publish your converters, report generators, annotation modules, gene mappers, and etc with one command to cravat store for other people to install and use also with one command or one click. There are 44 annotation modules as of today and more are being added.

Its GUI components are being rapidly polished but its command-line interface is quite stable. Let me know if you have any question or suggestion about open-cravat.

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open-cravat tool • 439 views
ADD COMMENTlink modified 4 months ago • written 6 months ago by slcrick120
gravatar for slcrick
4 months ago by
United States
slcrick120 wrote:

open-cravat 1.3.2 has been released. This version has the following updates:

Updates on Interactive Result Viewer (cravat-view):

  • Data loading indicator
  • Local filter select box
  • Show-all and hide-all buttons for widgets
  • Load filter of cravat-view now has two modes, simple and advanced, and it shows only the filter operators relevant to the type of the filtered data.
  • Widgets can be hidden by default and its show/hide status can be saved and loaded.

Updates on cravat web GUI (wcravat):

  • Store now has a Front Page with Most Downloaded and Newest modules.
  • Store shows annotator modules' source data version for provenance.
  • Store can sort modules by their name, size, and date of post.

Updates on cravat:

  • cravat detects input files’ encoding and reads them correctly and writes output files always in UTF-8.


  • Module updates have been concurrently released.
  • VCF format converter now supports VarScan VCF format.
  • Fixed various bugs.
ADD COMMENTlink modified 4 months ago • written 4 months ago by slcrick120
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