I've found a post explaining strand designations for some Illumina systems:
So the way they explain it is some local designation which is robust to reference genome build rearrangements. What confuses me is the supplementary of the following paper:
In Table 1 they list this as exclusion criteria on Illumina 370CNV:
Call rate <97%, HWE p<1-6, MAF <1%, Mishap p<1-9, A/T and G/C SNPs, Mismatches between Illumina, dbSNP and/or HapMap position
Why would anyone exclude A/T and G/C SNPs? (Also, what is mishap?)
Thanks in advance!