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Different ARO with or without -justDetermineActiveRegions for HaplotypeCaller
I noticed that for one BAM, when calling HaplotypeCaller (I am using version 3.5), with or without the -justDetermineActiveRegions, the ARO results are different at several intervals.
For example, one is (without -justDetermineActiveRegions vs with it):
413386,413388c413386,413388 < chr7 100550695 100550914 size=219 1.00000 < chr7 100550914 100550915 end-marker 0.00000 < chr7 100550914 100551155 size=241 1.00000 --- > chr7 100550695 100550944 size=249 1.00000 > chr7 100550944 100550945 end-marker 0.00000 > chr7 100550944 100551155 size=211 1.00000
This is quite not as expected. justDetermineActiveRegions make the map() return directly without doing any job. This should not affect the active regions if my understanding is correct. But the test shows it does. I may understand something wrongly here.
Could you please give some comments on why the behavior is like this?