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Old 01-20-2014, 05:24 PM   #1
Min Jung Lee
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Location: Seoul Korea

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

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.
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Old 01-20-2014, 05:27 PM   #2
Richard Finney
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Download and install CYGWIN ; include the gcc package when you install CYGWIN.

Compile samtools under cygwin.

Run samtools in cygwin command prompt shell.
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Old 01-20-2014, 06:15 PM   #3
Min Jung Lee
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Default 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...
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Old 01-20-2014, 09:10 PM   #4
dcameron
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The picard tools utility BuildBamIndex can be run on Windows if you have java installed.

http://picard.sourceforge.net/comman...#BuildBamIndex
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Old 11-20-2014, 02:39 PM   #5
ChrisRalps
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Thx for the suggestion dcameron. Now picard is here at github and I used this command:
Quote:
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.

Last edited by ChrisRalps; 11-20-2014 at 02:43 PM.
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Old 11-21-2014, 07:12 AM   #6
Baseless
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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.
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Old 11-21-2014, 12:06 PM   #7
ChrisRalps
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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.
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