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Illumina2preGS
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
Summary
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
Usage
illumina2preGS --snpfile <yourSnpFinalReportFilename>
The only mandatory argument that is required is the –snpfile
Other options can be modified with optional arguments:
Optional Arguments
--mapfile
File name for the map file. Default “SNP_Map.txt”
--genome
Indicate type of genome (1 - bovine, 2 - ovine)
--nosortmap
Genotype file will be in the same order as given
--gc <thr>
Set GC cutoff (thr) for exclude call (default from GenomeStudio 0.15)
--alphasize
Set the maximun length to store alphanumeric IDs (default 10)
--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
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
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
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.