Genome Studio confusing SNP allele coding schema, what is the main genotype of the sample?
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3.8 years ago
mittu1602 ▴ 180

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.

Illumina genomeStudio • 1.6k views
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