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?
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