For a positive selection test that I want to use I need the ancestral states of all SNPs present on my data.
I checked this FAQ from NCBI, followed the instructions and downloaded a file that contain the rsnumber, physical position and ancestral state of over 60 million SNPs. However as a simple test, when I try to match some SNPs present in my data based on the rsnumber and physical position I didn't get any match. But when I entered the SNP on the dbSNP website I could find the SNP with a putative ancestral state with a matching physical position.
The last upadte from the downloaded file is March 2014, but I couldn't find a reference to the build.
Are there other places where I could get the ancestral states of SNPs? Or find an updated file from dbSNP?
Thank you in advance.
EXTRA INFORMATION FOR COMMENT
Example of an rsSNP in my data:
This is an rsSNP present in my data with its physical position based on the GRCh37 assembly.
When I check the SNPAncestralAllele.bcp.gz file for this rsSNP I get these matches:
rs2823639 0 A
rs2823639 1050982 A
rs2823639 1052591 A
rs2823639 1056295 A
rs2823639 1056571 A
rs2823639 1061835 A
The information on the dbSNP website is however this:
Ancestral allele: A
The ancestral state is the same but the physical position is not.