[BioC] faster way to get differential calls from pileup?
wrighth at ohsu.edu
Sat Oct 16 20:54:46 CEST 2010
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
lanes in the future I'm curious if there's a faster or better way to
go about this sort of process. Thanks...
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