BAI files are included with the download when using the GDC Data Transfer Tool to download BAM files.
When using the API to download BAM files, BAI files will only be included if the related_files=true parameter is specified together with the BAM UUID, for example:
https://api.gdc.cancer.gov/data/53f4ad60-0777-409c-a34d-ca4442dc9c44?related_files=true
Alternatively, users can determine the BAI file UUID from the API files endpoint by supplying the BAM UUID. The BAI file UUID can then be used to download the BAI file from the data endpoint.
https://api.gdc.cancer.gov/files/53f4ad60-0777-409c-a34d-ca4442dc9c44?pretty=true&expand=index_files
https://api.gdc.cancer.gov/data/60cefd89-b428-46b7-b5b0-3b6e2743ab20
Note: BAI files are not available for sliced BAM files.