Attention: Want an end-to-end pipelining solution for GATK Best Practices?
In the picard CrosscheckReadGroupFingerprints command, it asks for a Haplotype_map file. What format does Haplotype_map file need to be in? If you have multiple BAM files with the same RG tag, would this command work? If not, what is the best way to edit 6000+ BAM files to have unique RG tag names?