> Given a BAM file e.g. x.bam the application is looking for the file
> x.bam.bai in the same directory. It sounds this is the case? If you create
> the index file with samtools :
> samtools index x.bam
> then it will create x.bam.bai. You could try re-creating the index with
> samtools.

I think the .bam file needs to be SORTED too (by reference coordinates)
before indexing. Chances are it already is sorted (as it was used with USCS)
but just in case:

% samtools sort original.bam original-sorted   # will
create original-sorted.bam
% samtools index original-sorted.bam

NOTE that for the sort command, you don't put the .bam suffix ... it does it
itself (ech).

--Torsten Seemann
--Victorian Bioinformatics Consortium, Dept. Microbiology, Monash
University, AUSTRALIA
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