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

[Dan Bolser]

2009/2/18 Johan Lindberg <johlin at kth.se>:
> Figure 5 in the paper  "Accurate whole human genome sequencing using
> reversible terminator chemistry" that Durbin is author of should answer your
> question.
> best regards,

Thanks for the reference.


> // Johan
>
> On 18 feb 2009, at 21.02, Dan Bolser wrote:
>
> 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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