Re: [Samtools-devel] [Picard] How get reads covering per base

[Alec W. <al...@br...>]

Hi Diego,

Try this: http://picard.sourceforge.net/javadoc/net/sf/picard/util/SamLocusIterator.html

-Alec

On Apr 12, 2013, at 6:25 PM, Diego M Salvanha <din...@gm...> wrote:

> Hi-
> 
> I am writing some Java code (using Picard) to integrate some piece of software to SAM files. Now what I need is having the number of reads covering the site (very similar to the pileup format output, where I have chromosome, reference base and number of reads covering the site).
> 
> I am mostly trying to find a class/function on Picard for doing so, so far no luck.
> 
> Does anyone know how to have the same result using any already implemented Picard classes ?
> 
> I do appreciate your time.
> Cheers.,
> Diego M Salvanha
> Grad. Student Inter-institutional Grad Program on Bioinformatics - University of Sao Paulo
> Member of LabPIB - http://labpib.fmrp.usp.br | Dr. Ricardo Z. N. Vencio
> Visiting Grad Student | Dr. Nitin Baliga's Group
> Institute for Systems Biology
> +1 (206) 732-1415 |  +1 (206) 407-8560
> 
> 
> 
> 
> 
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