reference alle is a major allele or a non-disease allele in VEP

Question

[tonja.r]

I am working right now with VEP and I got SNPs from one external paper that has only the following information: snp, chr, pos,gene, risk allele, non-risk allele, frequency for a risk allele

From MAF I can identify the major alleles and the minor allele. Sometimes a risk allele is a major allele.

Example:

rs28411352    1    38278579    MTF1-INPP5B    T    C    0.26

Meaning that T is a risk allele and a minor allele.

rs12140275    1    38633879    LOC339442    A    T    0.78

Meaning that A is a risk allele but T is a minor allele.

My question is what should I define for input for VEP as a reference allele a non-risk allele or a major allele?

PS. I also do not have a strand information but as soon as I define what a reference allele is, I can look up in the fasta file if my allele is represented with respect to positive strand or not.

Thank you in advance.

[gaurav.singh]

The strand of the alleles you give is specified in the 5th column, should be your reference allele