Re: [Samtools-help] pileup ace like format

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Sorry for the late reply. There is no such tool implemented in samtools,
but I think it should not be hard to convert pileup to CAF. Note that
the "^" and "$" symbols in pileup allow you to get each read
sequences. The i-th "^" corresponds to the i-th mapped read and thus you
can get read name.

In addition, how CAF is useful in your case? Could you show some
examples? Maybe we can think of other ways to achieve the goal without
generating CAF.

Thanks,

Heng

On Fri, Sep 18, 2009 at 01:15:41PM +0200, Jose Blanca wrote:
> Hi:
> I've aligned some sanger and solexa reads to a reference genome with bwa. I've 
> merged, sorted and pileuped the alignments. Now I have the bam and the pileup 
> files.
> 
> I would like to obtain a caf like alignment file (or a file with such 
> information). The information not present in the pileup file is the name, 
> nucleotide and quality of each individual read that contribute to the 
> consensus.
> 
> That information is very useful when reads originated from several 
> individuals/samples are aligned.
> 
> Is that posible? If it is not posible, could you give me some direction on how 
> could I program such tool?
> 
> Best regards,
> 
> -- 
> Jose M. Blanca Postigo
> Instituto Universitario de Conservacion y
> Mejora de la Agrodiversidad Valenciana (COMAV)
> Universidad Politecnica de Valencia (UPV)
> Edificio CPI (Ciudad Politecnica de la Innovacion), 8E
> 46022 Valencia (SPAIN)
> Tlf.:+34-96-3877000 (ext 88473)
> 
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