Hello, Claudia,
It may be that the haplotype chroms you mention are the answer
to the entire issue. Without a sampling of the SNPs in question, I
cannot be sure it is all that is going on.
The haplotypes chroms are alternate versions of the chromosomes
and when a SNP maps to several alternate versions, we still consider
that they are uniquely mapped in the genome.
best wishes,
--b0b kuhn
ucsc genome bioinformatics group
On 2/16/2012 12:52 PM, Claudia Moreau wrote:
> Hi,
>
> I'm trying to transfer my Illumina650K SNPs from hg18 to hg19. I asked UCSC
> for the common SNPs 135 (I enclose the settings I used) with my list of 540
> 078 rs and I got 549 117 SNPs so that 9805 rs are double in the final list
> given by UCSC tables. But about the common SNPs, it is written on UCSC
> website that "Common SNPs(135) - SNPs with>= 1% minor allele frequency
> (MAF), mapping only once to reference assembly." So is there a reason why
> I'm getting SNPs in double?
>
> Now if I give this list of 9805 SNPs again to UCSC with the same settings, I
> get back 11 641 SNPs and not the 20 000 something that I was expected if
> they were all SNPs in double.
>
>
>
> Moreover, SNPs in double seem to be something else completely as there chr #
> is something like "chr17_ctg5_hap1".
>
>
>
> I'm a little bit confused with all this. I would like to know if I did well
> to transfer my data from hg18 to hg19 or if there is something wrong in the
> results?
>
>
>
> Thanks,
>
>
>
> Claudia
>
>
>
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