Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
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!