I am performing a quality control on data genotyped with Illumina's Global Screening Array version 1.0. There are conversion files available on Illumina's website (https://support.illumina.com/array/array_kits/infinium-global-screening-array/downloads.html). I have applied an update of SNP identifiers with the use of the file 'Infinium Global Screening Array v1.0 Loci Name to rsID Conversion File (GRCh37)'. However, there are still unusual SNP identifiers (e.g., "GSA" or "chr" as prefix) and that are not updated yet. It seems that this file contains incomplete. Does anyone know whether there is a way to update all SNP identifiers?
(thanks in advance for input)