Illumina Manifest files - A1 vs. A2

Question

[rednalf]

While looking at Illumina's manifest files, I always see two versions for the same array: A1 and A2. What is the difference between the two? Is it that A1 always corresponds to GRCh37, and A2 to GRCh38?

[h.mon]

Which array are you looking at?

[rednalf]

I am looking at the GSAMD (Infinium Global Screening Array-24 v1.0 GSA + Multi Disease) array.

[h.mon]

https://support.illumina.com/array/array_kits/infinium-global-screening-array/downloads.html

For the manifest files, I found A2 and A6, but no A1. Apparently A2 corresponds to GRCh38 (the manifest file says GenomeBuild 38), and A6 corresponds to GRCh37 (the manifest file says GenomeBuild 37). Other files refer either to A1 or A6, but no A2. If this is important for you, you should contact Illumina support and ask for clarification.

Answer 1

[Giulio Genovese]

I have found that it is always the case that _A1, _B1, _C1 manifest files contain GRCh37 mappings and _A2, _B2, _C2 manifest files contain GRCh38 mappings. If you don't have an _A2, _B2, _C2 manifest file, you can remap the flanking sequences against GRCh38 using gtc2vcf