Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

GATK process banner

Need Help?

Search our documentation

Community Forum

Hi, How can we help?

Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more



1 comment

  • Avatar
    Kevin Lydon


    It appears that the documentation excerpt you shared is actually inaccurate.  VariantFiltration does not have an option to exclude the variants.  I'll make sure that documentation gets updated. 

    Having separate steps for filtering and removing variants is a deliberate choice for maintaining data provenance, as it allows you to keep a record of what variants were removed by what filters.  However, I think you make a valid point that it can be less efficient to create that intermediate file if you're not interested in retaining that information.

    If you would like to see that feature added to VariantFiltration, you can create a feature request issue on the GATK GitHub repo.

    Comment actions Permalink

Please sign in to leave a comment.

Powered by Zendesk