readme.illumina2pregs
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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 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
USAGE
<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
- -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
- -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)
- -alphasize - Set the maximun length to store alphnumeric 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: ** 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
readme.illumina2pregs.1401097682.txt.gz · Last modified: 2024/03/25 18:22 (external edit)