I have a big file (461580 rows) containing SNP positions, that looks like this :
1:58989 1:59155 1:59256 1:59260 1:59264 ... X:154396891 X:154396901 X:154397026 X:154397078 X:154427901
I want, as an output, the ancestral allele for each of these SNP.
I tried to work with Allele.bcp that you can find on ftp://ftp.ncbi.nlm.nih.gov/snp/database/shared_data/, as it is advised on the NCBI website (https://www.ncbi.nlm.nih.gov/books/NBK44409/). Unfortunately 1) I have issues to make sense out of this file and all the explanations I found are quite confusing, and 2) in any case it seems that I would need the rsID which I don't have.
I wonder if there is a simple way to get the ancestral SNP allele without knowing the rsIDs.
PS : important precisions, this is human data and I work on with the hg18 build.