I am running some analysis on bam files that I have downloaded from ICGC. I don't have the original fastaq files, just the bam. The bams was aligned using a different reference than the one I use in my pipeline - I use hg19 from UCSC, I am not sure which reference was used for the bam but I think this is the Ensmble reference. The result is different naming convention ('1' vs 'chr1', 'GL000241.1' vs 'chrUn_gl000241'), and different order of contigs. This causes problems, for example when working with GATK. What is the right way to handle such a situation?