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Error "Mate unmapped flag should not be set for unpaired reads" after RevertSam
Hi, I am following the Tutorial#6484, Reverting a bam file into ubam, which runs successfully. However, when I tried to apply MarkIlluminaAdapters, I got an error message of "Mate unmapped flag should not be set for unpaired reads". I ran ValidateSamFile on the ubam file and got a reported error of "INVALID_FLAG_MATE_UNMAPPED". I checked the read in the original file which has a flag of 0, indicating an unpaired read that is mapped onto the forward strand. It seems that RevertSam mis-process single-ended reads. Do I have to remove all reads with flag of 0 in my original bam file?