samtools on S3

Question

[tomkp75]

Hello,

I'm using samtools 1.10 to work on file stored in an S3 bucket. It seems that samtools downloads the index file even though I'm giving it vi the command line. Is there a way to refer to the index file that is stored on S3 on does samtools necessarily have to download it?

Thanks,

Tom

[JC]

How are you running this? Can you show the command? Samtools should use your local reference.