How to make .bam file to .bai file format under MS Window7 operating system?

[Min Jung Lee]

Hello dear!
I have a illumina Miseq instrument, and have several data already aligned, that file format is .bam.
But I can't use Linux operating system, I have MS window7.
I have to create .bai file for CNV analysis.
Please answer me what is best program make the .bai file from .bam file.

[Richard Finney]

Download and install CYGWIN ; include the gcc package when you install CYGWIN.

Compile samtools under cygwin.

Run samtools in cygwin command prompt shell.

[Min Jung Lee]

Thank you for your answer.

But.. I don't know how to use Linux, Unix language... T.T
In Korea, many people don't know that language.
Can you recommand another way? Sorry...

[dcameron]

The picard tools utility BuildBamIndex can be run on Windows if you have java installed.

http://picard.sourceforge.net/command-line-overview.shtml#BuildBamIndex

[ChrisRalps]

Thx for the suggestion dcameron. Now picard is here at github and I used this command:

java -jar picard.jar BuildBamIndex INPUT=URL/File-Link-to.bam OUTPUT=Name-for.bam.bai

So far by creating the BAI out of BAM over HTTP I have the problem that some work for example in IGV and some not. The not working files are smaller then the working ones. I don't know yet if the BAM files are corrupt, the HTTP connection is problematic or just Picard on my system does not work flawlessly.

[Baseless]

If everything else fails, you could grab an Oracle VirtualBox, install a userfriendly linux flavour, face your fears and use samtools.

I do not consider myself a penguin lover, but when it comes down to NGS analysis, the power of the linux shell, perl and easy access to standard tools the community is using quickly becomes a necessity.

[ChrisRalps]

In the past I already did use successfully samtools both in VirtualBox and in the Ubuntu flavor I like (Lubuntu). So this would be not the problem. I currently just have no powerful system for VirtualBox and can't install another OS. I hope in some weeks I will get my working PC. Will see if I can solve my problems with the Picard/HTTP/Win7 package before.