Range request to only download a BAM genomic interval

Former User of DNAx Community_46

Hi all,

 

using WDL I would like to fetch a section (chrom:start-end) of a bam.

 

I know I can do this using

 

```

samtools view "the.bam" "chrom:start-end"

```

 

nevertheless (am I wrong ?), before using the BAM, RAP will fetch the **whole** BAM in my session.

 

A much faster way would be to use `Range-Request` ( https://developer.mozilla.org/en-US/docs/Web/HTTP/Range_requests ) on the remote bam.

 

First, samtools can work with URLs if the remote bam is indexed and the server supports Range-request:

 

samtools view "http://www.abc.org/in.bam" "chrom:start-end"

 

 

Second, it looks that AWS supports Range-Requests : https://docs.aws.amazon.com/whitepapers/latest/s3-optimizing-performance-best-practices/use-byte-range-fetches.html

 

So my question is: is there a way to fetch a section of a BAM in my session without fetching the whole document ?

 

Thanks !

 

 

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