[Bioc-sig-seq] comparing Affy SNP arrays with deep sequencing ?

[Wolfgang Raffelsberger]

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.

Thank's in advance,
Wolfgang

 
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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