I have to work with some GWAS data from a previous collaborator and I have only the FinalReport file from Illumina. I've found several posts online on how to transform the FinalReport into PLINK compatible file (lgen, map, fam) but the posts are very old and some of the methods do not work. Is there any easy way to get PLINK files? Thanks!
Here the header of the final, divided in columns for readibility
[Header] GSGT Version 1.9.4 Processing Date 4/8/2015 10:57 AM Content humanomniexpress-24v1-0_a.bpm Num SNPs 716503 Total SNPs 716503 Num Samples 240 Total Samples 240 [Data] 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