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Picard AddOrReplaceReadGroups Error: Read CIGAR M operator maps off end of reference
I have bam files generated by Illumina's CASAVA pipeline, and the reference genome version in the accompanying document is 'NCBI37_UCSC'. when I use GATK RealignerTargetCreator to do Local realignment, I meet a problem --"do not have RG". so I use Picard AddOrReplaceReadGroups to add RG, but I also meet an problem --"Read CIGAR M operator maps off end of reference", how can I resolve it?? thank you very much!