I have extracted some genome wide association information from consortium results for a list of SNPs i'm interested in. The results are based on positive strand of build GRCh36. I have no problems updating rs numbers, and position using a combination of biomaRT and liftOver. However i am unsure on how to assign alleles. Now i know that biomaRT allele information is all on the positive strand. This is an easy task for un-ambiguous SNPs (e.g C/T, A/G). For ambiguous SNPs i.e (C/G and A/T) I can assign alleles based of matching allele frequencies, but this might become more difficult for SNPs with minor allele frequencies close to 0.5. More so since biomaRT gives you overall MAF across all populations while the consortium MAFs are for Europeans only.
The ideal solution would be to know whether the strands have changed between builds for my list of SNPs (e.g build 36 to 37 and/or build 37 to 38). Can such information be found? Am i missing an obvious solution to this problem?