Help Creating a .vam.bai file

[Desiree Wilson]

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?

[Desiree Wilson]

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.

[maubp]

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

[Desiree Wilson]

Thank you so much. I will try this. Thank you, maubp.