Hi,

I have downloaded publicly available SNP data genotyped on the 777k BovineHD array from Illumina. The SNPs are mapped to the last genome assembly (UMD3.1) and I would like to re-map them to the new assembly (ARS-UCD1.2).

I have found a data repository that contains files with all the variants from various genotyping arrays mapped to the new assembly. Among them is a .map file which has the updated positions associated with the new assembly, as well as updated allele files.

Using plink and the --update-map function, I have updated the positions of the majority of the SNPs with only minor loss. The issue I have is that when I try to use the --update-alleles function with the updated allele file in the repository mentioned above, almost all of alleles fail of update and are logged to a .allele.no.snp file. I am doing this on the .bed, .bim and .fam files generated from the first plink command.

Is there something I am not doing correctly or am I missing a step in this procedure? Thanks.