2009/2/18 Wolfgang Raffelsberger <[email protected]>: > Dear List, > > here I have a more general question : > Has anyone compared (directly?) Affy 500kSNP arrays with deep sequencing > (here I'm rather thinking of Solexa/Illumina) ? > How much sequencing coverage should allow a 'decent' SNP calling ? (Maybe I > need to add that heterozygous SNPs should be detected, too) > At which level (of coverage) would you expect to get equivalent or better > results as Affy SNP arrays ? (Of course I know that a few (specific) SNPs > may be lost due to the random distribution of the reads...) > > Or a variant of the question, if one sequenced a given zone of high interest > (possibly with multiplexing) what would be current advice in terms of size > of the zone (and number of multiplexed patients) to get suffient coverage to > detect heterozygous SNPs.
Richard Durbin did some calculations to look at this question, namely, how much depth do you need over a SNP to call it with 99.9% accuracy... how much coverage do you need to get that much coverage on you SNP with 99.9% accuracy... Sadly I don't have the figures to hand, but perhaps you can email him this question and post the answer back to the list? Dan. > Thank's in advance, > Wolfgang > > > . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . > Wolfgang Raffelsberger, PhD > Laboratoire de BioInformatique et Génomique Intégratives > CNRS UMR7104, IGBMC 1 rue Laurent Fries, 67404 Illkirch Strasbourg, > France > Tel (+33) 388 65 3300 Fax (+33) 388 65 3276 > wolfgang.raffelsberger (at) igbmc.fr > > _______________________________________________ > Bioc-sig-sequencing mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
