Finally had time to try this, you we're absolutely right Peter! Running a
sort on the .bam file fixed our problem.
Thanks a lot, now we have a lot of work to do :)
Cheers,
/Stefan
On Fri, Feb 13, 2015 at 3:43 PM, Peter Cock <p.j.a.c...@googlemail.com>
wrote:
> On Fri, Feb 13, 2015 at 1:55 PM, Stefan Nordlander
> <stefan.o.nordlan...@gmail.com> wrote:
> > Greetings samtools-list members,
> >
> > I'm assisting an associate with some calculations, and we've run into
> some
> > problems with samtools.
> > What I'm trying to do is to generate a .bai index file but I get the
> > following error message:
> >
> > NO_COOR reads not in a single block at the end 0 -1
>
> If your BAM file is sorted, then all the reads with no POS
> value (i.e. NO_COOR) should be at the end. Are they?
>
> > I found the suggestion to add -c to samtools which did not help. I also
> > found at http://sourceforge.net/p/samtools/mailman/message/33155863/ the
> > suggestion that samtools only supports chromosome length of 512Mbp for
> index
> > generation. However our longest chromosome is +248Mbp, far from 512Mbp.
> >
> > Any help would be appreciated!
>
> Yes, this does not look like a problem with the reference length.
>
> Peter
>
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