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

[Dan Bolser]

2009/2/18 Wolfgang Raffelsberger <wraff at titus.u-strasbg.fr>:
> 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
>
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