The Frontline Support team will be offline February 18 for President's Day but will be back February 19th. Thank you for your patience as we get to all of your questions!
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.