[BioC] Strand information for dbSNP packages

[Valerie Obenchain]

Hi Alex,

On 02/28/2012 03:03 AM, Alex Gutteridge wrote:
> I notice the GRanges returned by the dbSNP packages have strand '*'.
> Does anyone know how safe am I in assuming that the variant alleles
> also given by the package actually correspond to the '+' strand?

The dbSNP packages don't contain any strand information so it isn't safe
to assume one strand or the other.
>
> I ask this in the context of trying to use predictCoding in the
> VariantAnnotations package to find coding SNPs. For SNPs in genes on
> the '-' strand I have found that I have to complement the alleles
> given by dbSNP to get the correct result. I just want to make sure
> that assuming the alleles are from the '+' strand is a reasonable
> assumption in the vast majority (>99%) of cases.

This does not seem right, I'll look into it.

Valerie
>
> I realise from my reading of the SNPlocs.Hsapiens.dbSNP.20110815
> manual that some SNPs will be incorrect anyway (it mentions ~0.1% of
> SNPs not mapping to the reference at all), that level of failure is
> acceptable, but anything higher would be a worry.
>