[Genome] HAPMAP SNP question

[Brooke Rhead]

Hello Travis,

I spoke to one of the developers here who helped make the HAPMAP SNPs 
track in the Genome Browser, and he did not have an answer to your 
question.  He suggested that you contact the HapMap Project directly, 
which you have already done.  I'm sorry we cannot be of more assistance 
in this case.

--
Brooke Rhead
UCSC Genome Bioinformatics Group


Travis Ptacek wrote:
> I have emailed HAPMAP's tech support people with this question and
have yet to recieve a reply. I thought that one of you might have an answer.
> 
> The question is this: Why are monomorphic SNPs and SNPs with genotype
> data missing for several populations included in the HAPMAP SNP data set?
> 
> The published HAPMAP papers made it sound like they attempted to
genotype every dbSNP SNP that an assay could be designed for, and
included every SNP that passed their QC standards. I.e. it looked like
SNPs that were monomorphic and SNPs with inclomplete genotype data
passed QC.
> 
> I just wanted to confirm that their exclusion criteria was this
general, because the disparity between HAPMAP SNPs and dbSNP SNPs (in
the CFTR region, ~200kb, ~260 HAPMAP SNPs vs ~900 dbSNP SNPs) suggested
more stringent criteria to me.

> Thanks in advance,
>  
> Travis Ptacek
> 
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
> http://www.soe.ucsc.edu/mailman/listinfo/genome