Hi
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?
Thanks
Abhishek