Illumina final report file to PLINK

Question

[f.abbondanza94]

Hi everyone,

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