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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