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  • 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?

  • #2
    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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    • #3
      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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      • #4
        Thank you so much. I will try this. Thank you, maubp.

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