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How is "ALLOW_N_CIGAR_READS" implemented in GATK4?

I'm running ASEReadCounter from GATK4. In the GATK versions prior to 4, there is parameter "-U ALLOW_N_CIGAR_READS" which is necessary for processing RNA-Seq alignment. However -U is not available any more in GATK4. Is there another parameter that controls this in version 4?


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