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A program to convert genomic information from Illumina files for the BLUPF90 family of programs

Ignacio Aguilar - INIA Las Brujas

email: iaguilar at

02/10/11 - 06/16/12


Tool for converting FinalReport and SNP_Map.txt files from Genome Studio into files suitables for reading with pregsf90

Reads only AB codes and generates integer variable 0,1,2 or 5 for missing


illumina2preGS --snpfile <yourSnpFinalReportFilename> 

The only mandatory argument that is required is the –snpfile

Other options can be modified with optional arguments:

Optional Arguments


File name for the map file. Default “SNP_Map.txt”


Indicate type of genome (1 - bovine, 2 - ovine)


Genotype file will be in the same order as given

--codeab  <n>

Indicate column number for the first allele with code AB (defalut 7)

--gc  <n thr>

Set column number (n) of GC and the cutoff (thr) for exclude call (default from GenomeStudio 0.15)


Set the maximun length to store alphanumeric IDs (default 10)


Set a file name for output SNP file (default snps2pregs)

File formats

Input files


 1 Index                                             
 2 Name                                              
 3 Chromosome                                        
 4 Position                                          
 5 GenTrain                                          
 6 Score                                             
 7 SNP                                               
 8 ILMN                                              
 9 Strand                                            
10 Customer                                          
11 Strand                                            
12 NormID


 1 SNP_Name
 2 Sample ID
 3 Allele1 - Forward
 4 Allele2 - Forward
 5 Allele1 - Top
 6 Allele2 - Top
 7 Allele2 - AB
 8 Allele1 - AB
 9 GC Score
10 X
11 Y

** this is the default column position but you can use –codeab argument for change it the column for

Output files


 1  ID (alphnumeric identification of lenght "alphasize", default 10)
 2  one space
 3  genotypes: 0, 1, 2, for AA, AB and BB respectively and 5 for missing.


 1 index
 2 chromosome
 3 position 
 4 name 
 5 index in original SNP_Map.txt

SNP without defined position (CHR = 0) in the SNP_Map.txt will be located in a new CHR 32 in the output snp_map, but still with 0 position.

readme.illumina2pregs.txt · Last modified: 2018/05/21 15:47 by ignacio