Question: reference alle is a major allele or a non-disease allele in VEP
gravatar for tonja.r
3.4 years ago by
tonja.r430 wrote:

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.

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.


snp • 2.4k views
ADD COMMENTlink modified 3.4 years ago • written 3.4 years ago by tonja.r430

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

ADD REPLYlink written 3.4 years ago by gaurav.singh10
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