Illumina And Symmetric Snps Problem

Question

[Joey]

Can someone explain me the issue with Illumina and symmetric SNPs i.e. SNPs with A/T or C/G? I have read quite a few papers which excludes these symmetric SNPs because of strandedness issues.

Thanks,

-Joey

Answer 1

[Matt Shirley]

See this technical note from Illumina. The basic issue is that Illumina always designates A or T as allele "A", and C or G as allele "B", unless there is an A/T or C/G, in which case the surrounding sequence is evaluated to determine which nucleotide is allele "A" and which is "B".