I have access to some indexed BAM files in S3. Using the AWS CLI, it is fairly easy to download the entire BAM file. That was fine for our initial analysis, but for validation, we are interested in looking a small region of ~10kb in thousands of individuals.
The BAM files are indexed and S3 supports GET requests with range headers so this should be possible. Does anyone know of a tool that does this?
EDIT: htslib 1.3 was recently released and supports random access to BAM files in s3.