Bam File Readers That Can Read Remote Ftp/Http Files?

Question

[14134125465346445]

What bam file readers that can read remote ftp/http files? I only know of samtools, but I would like to know of other tools that can also read remote files through ftp/http or other protocols. By remote access, I mean something like this:

samtools view ftp://ftp.site.com/file.bam chrN:1234-3456   
samtools view http://www.site.com/file.bam chrN:1234-3456

Answer 1

[biocyberman]

I am not aware of those tools. However you can easily combine wget, curl, lftp or any download tools with samtools in a shell, perl, or python script to get the job done.

[Istvan Albert]

that is not the same thing because you don't need to download the entire file to do a remote viewing - whereas your solution does that - the downloads could be impractically large

[biocyberman]

You are right, about the possibility of viewing files without download the whole things. But from my experience, it is better to load everything to my workstation and do whatever I like afterward.

Answer 2

[Chris Miller]

I believe IGV will read remote files via http or ftp

[biocyberman]

Chris, how does IGV work for you when you view a very large SAM file, i.e whole exome? I have 24GB of RAM on a workstation and the software works at unacceptable speed.