Re: [Samtools-help] problem with indexing

[Tom B. <tb...@um...>]

Before indexing, the records in a .bam file must be sorted by 
position ("coordinate").  Use 'samtools sort'.  That's probably 
the issue here.  This email just now came through to the list.

 	 	 	 	 	 	-  tom blackwell  -

On Fri, 28 Jan 2011, Christos Kozanitis wrote:

> Hi
>
> I am trying to index a 6GB bam file of Illumina data, which was originally in export format and was converted to sam by export2sam.pl.
>
> However the bai file that I obtain has a size of 40 bytes and when I run: "view sam_sorted.bam chr3" I get only 27 reads in the output (out of the 21M reads that I expect).
>
> Is there any step that I have skipped in the procedure?
>
> My version of samtools is 0.1.6.
>
>
> Thanks
> Christos
>
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