Output active regions in GATK4 HaplotypeCaller
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?