Hi ,

I have downloaded the Affy6.0 snp annotation file from Affy website but the snps are maped to an old build. for example, rs2834296 is mapped to chr 21 and base pair position 34203263, but if you go to Ensembl you will find this snp has a different name rs4591 and the base pair is  35281393.
I needed to remap all the snps to the current build so I tried biomart package using R using the scrip below

mart <- useMart("snp")
 mart<-useDataset("hsapiens_snp",mart)
out=getBM(attributes=c("refsnp_id","chr_name","chrom_start"),
 filters=c("refsnp"), values=snps, mart=mart)


here is the problem

snps is  a vector of rs# from the Affy 6.0 ( there are about 900,000) snps but the script took forever was never finished.
I tried to have the vector  snps to be the only the rs# from chr 21, but not all the snps get mapped for example the above snps that i mentioned before  rs2834296 will be dropped.


any ideas on how to map the snps in the affy 6.0  to the current build

thanks and appreciate your help


      
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