I know there's another question along the same lines, but I suspect my situation is slightly different...
I have an Illumina Final Report file, but I don't have access to Illumina directly, so I have to work with the file I have or I have to request one with more columns from someone else. My Final Report files have these columns:
SNP Name Sample ID Allele1 - Top Allele2 - Top GC Score Sample Name Sample Group Sample Index SNP Index SNP Aux Allele1 - Forward Allele2 - Forward Allele1 - Design Allele2 - Design Allele1 - AB Allele2 - AB Allele1 - Plus Allele2 - Plus Chr Position GT Score Cluster Sep SNP ILMN Strand Customer Strand Top Genomic Sequence Plus/Minus Strand Theta R X Y X Raw Y Raw B Allele Freq Log R Ratio CNV Value CNV Confidence
From reading other questions, I believe I need to produce three files: a .lgen, a .map, and a .fam. My main question is this, I suppose: which columns do I use to produce each file?