Given the uptake of CRAM as a major data format in ENA, we have launched a new comprehensive service to provide reference coordinate-based indices for CRAM data. CRAM index files (CRAIs) are constructed as part of CRAM submission processing and presented alongside their corresponding CRAM files through existing data discovery and retrieval services. The CRAM index files are available from the same directories as their corresponding CRAM files.

More information about the generated CRAM index files is available at:
http://www.ebi.ac.uk/ena/submit/read-file-formats#cram_format