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?