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readme.illumina2pregs

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.

readme.illumina2pregs.txt · Last modified: 2019/09/27 00:36 by ignacio