Broken GATK 3 documentation links

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Harly Durbin

• March 16, 2020 19:18

Hiya! I posted on Twitter a few days ago about broken links to some of the GATK 3 tool docs (https://twitter.com/harlyjaned/status/1238564654957441025?s=20) and Geraldine asked that I share some examples to the forum and have someone tag her. 

Here are a few that I ran across:

https://www.broadinstitute.org/gatk/guide/tooldocs/org_broadinstitute_gatk_tools_CatVariants.php

https://www.broadinstitute.org/gatk/guide/tooldocs/org_broadinstitute_gatk_tools_walkers_variantutils_CombineVariants.php

https://www.broadinstitute.org/gatk/guide/tooldocs/org_broadinstitute_gatk_tools_walkers_variantutils_VariantsToTable.php

https://software.broadinstitute.org/gatk/guide/article?id=3225

https://software.broadinstitute.org/gatk/documentation/tooldocs/3.8-0/org_broadinstitute_gatk_tools_walkers_haplotypecaller_HaplotypeResolver.php

 

Hope that helps!

 

 

 

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  Bhanu Gandham

  • March 18, 2020 22:03

  Hi Harly Durbin

  Geraldine is working on fixing broken links to articles. She is currently working on an O'Reilly book about GATK and genomics that's coming out in a few weeks. And so might take a few days to fix this. In the mean time a workaround for this is to replace "guide" with "documentation" in the url and it should work. Example: https://software.broadinstitute.org/gatk/documentation/article?id=3225

  Unfortunately, we will not be able to redirect links to tool documentation. For that you will have to go to this github repo of our archived documentation: https://github.com/broadinstitute/gatk-docs/tree/master/gatk3-tooldocs
  
  

   

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