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I am woking right now with a VEP and I got SNPs from one extern 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 alle 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.
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 alle 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.