Help with Samtools "view"

[Ash]

Hi guys,

Apologies up front if this is a stupid question... I've been using the following to view areas of bam alignments, which is really convenient as it allows me to check that my region of interest has read coverage

$ ./samtools tview ftp://blahblahblah.bam ref.fasta

So far this has been great as it allows me to view the information without having to download it all to my computer. However, I have a number of regions in the genome to check, and reading through the manual, I thought that the "view" option may be more useful and allow me to extract what I need without having to look at each site of interest individually. So I tried the following:

$ ./samtools view ftp://blahblahblah.bam chr5:8932800-8932900

and the answer that I got was:

$ fail to get the reference name. Continue anyway.

so I figured that it needed some kind off reference seqs, like tview does, so tried:

$ ./samtools view ftp://blahblahblah.bam -t ref.fasta chr5:8932800-8932900

but I'm still getting the same answer. Is this because the "view" option of samtools can't use files not located on my computer? Or am I missing something?

All help gratefully received!

A

[Ash]

Problem solved! It wasn't liking the "chr5" bit - this is 1000 genomes data and they just use 5 instead of chr5.