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Table of Contents
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
The following fields should be present in the SNP_Map.txt file,
Any order of columns is supported.
Column positions will be assumed based on the keywords:
- Name
- Chromosome
- Position
Other fields will be ignored
FinalReport.txt
The following fields should be present in the Final Report file, Any order of columns is supported.
Column positions will be assumed based on the keywords:
- SNP_Name
- Sample ID
- Allele2 - AB
- Allele1 - AB
Optional fields:
- GC Score
Other fields will be ignored
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.