On Oct 16, 2010 2:55 PM, "Hollis Wright" <wrighth@ohsu.edu> 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
> lanes in the future I'm curious if there's a faster or better way to
> go about this sort of process. Thanks...
>

Hi, Hollis.  Have you considered converting to VCF format and using some of
the VCF tools for this type of thing?  With VCF, you get one row per locus
with the genotypes for all your samples in that row.  Conversion to
tab-delimited text is also possible for processing in R.  I think Vince
Carey was looking into R tools for working with VCF, but I don't know where
that work stands.

All that said, several hours for finding overlaps sounds like a long time
for a couple of pileup outputs from exome sequencing.

Sean

> Hollis Wright
>
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