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Old 03-15-2012, 08:18 AM   #1
Desiree Wilson
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Location: Texas

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Default Help Creating a .vam.bai file

I downloaded a sample .bam file from the 1000 genomes server. I tried to visualize the .bam file into IGV and received the following error message:
Could not load index file for: <the .bam file path>. An index file is required for SAM & BAM files.
So I figured I needed to make the .bam.bai file myself.

I tried to create the index BAM file by typing the following line of code in R :
indexBam(file="<path to the .bam file>")
and received the error message:
No such file or directory....failed to build index

What am I doing wrong? Why can I not create this .bam.bai file?
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Old 03-15-2012, 10:01 AM   #2
Desiree Wilson
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Can someone point me to the direction of some reference material that can help? I've read Rsamtools vignettes and they aren't very helpful.
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Old 03-15-2012, 10:38 AM   #3
maubp
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Do you have samtools installed? R might be using that internally... But it might easier here to call samtools directly at the command line shell with:

samtools index example.bam
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Old 03-15-2012, 01:26 PM   #4
Desiree Wilson
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Thank you so much. I will try this. Thank you, maubp.
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