Opening non indexed BAM file

[Itay.zemach]

Hi all

I just recieved 11.5GB BAM file and I want to view these sequences.
I read that first i need to index the file and just then to view it in IGV or Genome Workbench. I am really stuck while trying to index it.
I read that i need to download samtools so i downloaded it but I cant index it.
I am win7 64bit user with no bioinformatic knowledge so please help me to understand how to index the file

Thanks in advance

[dpryan]

Saying you can't do something isn't enough information to help you with anything. Do you receive an error message? What is the command you're trying?

[crazyhottommy]

you need to sort the bam file first and then index it with samtools

[svural]

if you have access to any unix like machine, you can index it like

samtools index SAMPLE.bam SAMPLE.bai

And for IGV, keep both bam bai files in the same directory, IGV will find bai file when you ask it to open bam file.

[Itay.zemach]

can you recommend for unix like machine to download

if you have access to any unix like machine, you can index it like

samtools index SAMPLE.bam SAMPLE.bai

And for IGV, keep both bam bai files in the same directory, IGV will find bai file when you ask it to open bam file.

Can you recommend for unix like machine to download?

[crazyhottommy]

Can you recommend for unix like machine to download?

BioLinux would be great for you

http://nebc.nerc.ac.uk/tools/bio-linux/bio-linux-7-info

[RDW]

If you downloaded samtools from the official samtools page on Sourceforge, you probably just got source code, which is hard to use on Windows. However, there's an unofficial executable version for Windows here:

http://bow.codeplex.com/releases

Hopefully this will do what you want (I haven't used it, except to see if it runs). Unzip the download, put samtools.exe and the bam file in the same directory, navigate to that directory from the Windows command prompt, and run samtools from the prompt as in the unix example above.

[Itay.zemach]

Thank's RDW
I will try it and answer ASAP