Hello All, Many similar questions are earlier discussed here, but the confusion still remains same for me. Example from Output file of Genome Studio:
SNP rs2986164 Sample XYZ Allele1-Top A Allele2-Top G Allele1-Forward A Allele2-Forward G Allele1-Design T Allele2-Design C Allele1-AB A Allele2-AB B Allele1-Plus A Allele2-Plus G Chr 1 Position 25622291 SNP [T/C] ILMNStrand BOT CustomerStrand TOP Plus/Minus -
So which allele is to be considered specifically with respect to dbSNP, and why? and what if dbSNP database studies a specific strand on reverse strand, do they need to be flipped by PLINK (why?, the forward allele column takes care of it right?) It is confusing! Your answers with explanation will be acknowledged. Thank you.