[BioC] faster way to get differential calls from pileup?

[Martin Morgan]

On 10/16/2010 11:54 AM, Hollis Wright wrote:
> Hi, all; I've got a pair of lanes of exome sequencing data; we've  
> generated pileup files from samtools and we're interested in looking  
> for discordant calls for quality control or snp discovery. As best I  
> can figure out the way to do this involves doing a findOverlaps and  
> the programatically iterating through the match matrix to get the  
> matching positions and check for differences. However, the overlap  
> finding takes several hours, and since we anticipate there being many  

This sounds like it's taking longer than findOverlaps should be taking;
perhaps you are running out of memory (so process in batches, e.g., by
chromosome) or doing something inefficiently. What does your code look
like (simplified, if possible...)

Martin

> lanes in the future I'm curious if there's a faster or better way to  
> go about this sort of process. Thanks...
> 
> Hollis Wright
> 
> Sent from my iPhone
> 
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