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

Ignacio Aguilar - INIA Las Brujas email: iaguilar at inia.org.uy 02/10/11 - 06/16/12

Tool for converts FinalReport files from Genome Studio into file suitable for reading with pregsf90 Read only AB codes and generates integer variable 0,1,2 or 5 for missing

 <file> illumina2pregs --snpfile <yourSnpFinalReportFilename> <\file>

 the only mandatory argument that is required is the --snpfile
 other options can be modified with optional arguments:

Optional Arguments

1. -mapfile - File name for the map file. Default “SNP_Map.txt”
2. -genome - Indicate type of genome (1 - bovine, 2 - ovine)
3. -nosortmap - Genotype file will be in the same order as given
4. -codeab <n> - Indicate column number for the first allele with code AB (defalut 7)
5. -gc <n thr> - Set column number (n) of GC and the cutoff (thr) for exclude call (default from GenomeStudio 0.15)
6. -alphasize - Set the maximun length to store alphnumeric IDs (default 10)
7. -snpfile_out - Set a file name for output SNP file (default snps2pregs)

File formats:

Input files

SNP_Map.txt:

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

FinalReport.txt: ** this is the default but use –codeab for change it

 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

Output files:

snps2pregs:

 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.

snp_map:

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