Re: [Samtools-help] NO_COOR reads not in a single block at the end 0 -1 even though longest chromosome is only +249Mbp

[Peter C. <p.j...@go...>]

On Fri, Feb 13, 2015 at 1:55 PM, Stefan Nordlander
<ste...@gm...> 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