On Mon, 5 Oct 2009, Angie Hinrichs wrote:
> For Watson, the file > ftp://ftp.hapmap.org/hapmap/jimwatsonsequence/watson_snp.gff.gz was > downloaded and all SNPs in the file were kept. > The Watson data is not as simple as it should be. I recorded all that were in this file, but it is missing many SNPs. They kept the APOE out on purpose, but that doesn't explain the fact that there are only 2 million SNPs instead of the 3 million they report in the paper, and submitted to dbSNP. The ones in dbSNP lose the allele information, as the reference nt is reported whether it was found in Watson or not. And the 2 million is NOT a simple subset of the 3 million (the 2M has thousands of SNPs not reported in the 3M set). Just to keep it more confusing Ensembl made their own calls from the available reads and produced a third set of SNPs that doesn't agree with either of the others. Belinda _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
