Test-drive the GATK tools and Best Practices pipelines on Terra

Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

Output active regions in GATK4 HaplotypeCaller

virtuabhi123virtuabhi123 United StatesMember
edited January 2017 in Ask the GATK team


What would be the best way to output active regions from GATK4 HaplotypeCaller?

In GATK 3.x, an option --activeRegionOut <file name> could be used to write active regions in a TSV file. However, I am not able to find a similar option in GATK4 (September 2016 version commit id - b24fb75bf474d87f5e2259617fef268a145b28c6). The most similar option seems to be -justDetermineActiveRegions <boolean>, but it is not writing (or generating) active regions to a file.

I can also edit the code to add this option - is callRegion method (in HaplotypeCallerEngine.java) the right place to put it?



  • shleeshlee CambridgeMember, Broadie ✭✭✭✭✭

    Hi @virtuabhi123,

    This is an engine feature that has not been ported to GATK4. Is this something that you feel is important to your research?

    Also, we have not validated HaplotypeCaller in GATK4. For your research, please use GATK3.7.

Sign In or Register to comment.