tview error- "fail to load BAM index"

[iwtwb8]

Hello all, I'm getting this error when I attempt to run the following command with samtools:

"$ samtools tview chrom5.sorted.bam chrom5.fas

[bam_index_load] fail to load BAM index."

I'm able to do other things with the .sorted.bam file, like use the pileup command. Any ideas or suggestions?

[brpet]

samtools index chrom5.sorted.bam

will create a bam index (*.bam.bai file)

If you haven't done it before, this might be the problem

[iwtwb8]

Yes, that indeed fixed the problem.
So, in the "teach a man to fish" vein, what exactly does the index command do? I saw that it created the .bam.bai file, which was only 12 KB. The documentation in the manual for the command is as follows:


"index samtools index <aln.bam>

Index sorted alignment for fast random access. Index file <aln.bam>.bai will be created."

Just curious what the general purpose of this command is. I was able to run the pileup command with just my .sorted.bam file, without first running index. Is there a general way to know if you need the .bam.bai file?