I forgot to mention that vcf2sm was used to construct the data elements of the ceu1kg experimental data package -- approx 8 million snp calls on each of 60 individuals; with expression data on 41 individuals from the GENEVAR archive. ceu1kg also includes GRanges instances annotating locations and names of the SNP. On Sat, Oct 16, 2010 at 6:23 PM, Vincent Carey <stvjc at="" channing.harvard.edu=""> wrote: > On Sat, Oct 16, 2010 at 5:14 PM, Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: >> On Oct 16, 2010 2:55 PM, "Hollis Wright" <wrighth at="" 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. > > there is a vcf2sm function in GGtools "devel" branch (should get to > release with luck this monday). ?the intention is > to take a compressed tabix-indexed vcf file (as distributed by 1000 > genomes, specifically) and create a snpMatrix snp.matrix instance for > genotype calls on a chromosome for all individuals archived in a file. > ?the current code was written a while ago > and emphasizes small footprint, with a naive piping interface assuming > tabix installed and trivially accessible. ?there is much more > information available in VCF that this code makes no effort to > extract. ?some discussion of VCF harvesting would be in order at the > Heidelberg developer meeting, and comments from interested > developers/users are welcome. > >> >> 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 >>> >>> Sent from my iPhone >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> ? ? ? ?[[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >> >