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How active regions are identified
Dear GATK team,
I am looking into the code of GATK 4.0 and trying to understand how active regions work and are used. Are active regions only those containing substitutions and/or indels? If a region contains only reads that perfectly map on the reference genome, is this still an active region? Is there any realignment in such region?
I cannot find in the code if/where read perfectly mapping on the reference are filtered out from active regions.