This site is now read-only. You can find our new documentation site and support forum for posting questions here.
Be sure to read our welcome blog!
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!