05 December 2015

Happy birthday my blog. You are now ten-year-old.

Happy birthday my blog. You are now 10-year-old.

03 December 2015

GATK-UI : a java-swing interface for the Genome Analysis Toolkit.

I've just pushed GATK-UI, a java swing interface for the Genome Analysis Toolkit GATK at https://github.com/lindenb/gatk-ui. This tool is also available as a WebStart/JNLP application.


Why did you create this tool ?

Some non-bioinformatician collaborators often want some coverage data for a defined set of BAM, for a specific region...

Did you test every tool ?


How did you create an interface for each GATK tool ?

Each tool in the GATK is documented in a web page: https://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_gatk_tools_walkers_variantutils_SelectVariants.php and
each web page is associated to a structured JSON page https://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_gatk_tools_walkers_variantutils_SelectVariants.php.json

  "summary": "Select a subset of variants from a larger callset",
  "parallel": [
      "arg": "-nt",
      "link": "http://www.broadinstitute.org/gatk/guide/tooldocs/org_broadinstitute_gatk_engine_CommandLineGATK.php#-nt",
      "name": "TreeReducible"
  "activeregion": {},

This json is transformed to XML in order to process it with XSLT . A XSLT stylesheet generates some java code

That's it,