New (private) read filter that can revert the MQ of reads affected by indel realignment.

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In the process of realignment we add +10 to the MQ of each realigned read, breaking the MQ 60 cap. That may contribute to problems observed by Bertrand (a step in the ROC curve plot of the VQSR results)

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Ami Levy-Moonshine 2015-01-30 13:31:15 -05:00 committed by Geraldine Van der Auwera

parent a77c8dd421

commit bb76821942

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