geWorkbench

Protocol for managing and analyzing the SAEC data

Data reformating for PLINK

1. Get the information about the mapping between Illumina names and GSK names

from "PGX40001_GSK_SJS_B137_29Aug2007_DNAReport.xls" take columns B and C (DNA name, Subject ID) and store it into "mapping_info.txt".

2. take the four csv files provided by GSK and extract data per individual extractPatients.pl

 perl extractPatients.pl -outfile test.out -outdir ..\data -infile "..\SJS Delivery from GSK\PGX40001_Illumina1M\Extracted Genotypes\PGx40001_12278-DNA.csv"
 perl extractPatients.pl -outfile test.out -outdir ..\data -infile "..\SJS Delivery from GSK\PGX40001_Illumina1M\Extracted Genotypes\PGx40001_GSK_SJS_B137_28Aug2007_Genotype_Report_12914-DNA.csv"
 perl extractPatients.pl -outfile test.out -outdir ..\data -infile "..\SJS Delivery from GSK\PGX40001_Illumina1M\Extracted Genotypes\PGx40001_GSK_SJS_B137_28Aug2007_Genotype_Report_12277-DNA.csv"
 perl extractPatients.pl -outfile test.out -outdir ..\data -infile "..\SJS Delivery from GSK\PGX40001_Illumina1M\Extracted Genotypes\PGx40001_GSK_SJS_B137_28Aug2007_Genotype_Report_12276-DNA.csv"

3. sanity check: count all non-comment lines for a sample individual

$ gawk '!/^#/{print $1}' ../data/42.txt  |sort -u |wc
1069083 1069083 10938646

4. Generate the phenotype information copy columns (SubjectID, SEX, SBTY) from C:\SAEC\SJS Delivery from GSK\PGX40001_Clinical\Page1_4_5_7a_8a_9a_10_11_13a.txt to file phenotype.txt

If we need to use other phenotypes we can easily create other phenotype files that can be read in by PLINK separately and we don't need to generate the ped files again!

5. Generate the .map file for PLINK

In Locus_Annotation_Files>
gawk '{print $2 "\t" $1 "\t" $4 "\t" $3}' Human1M_Physical_and_Genetic_Map_Coordinates.txt > illumina1M.map

6. generate .PED file for PLINK makePED.pl

perl makePED.pl -mapfile mapping_info.txt -snpfile snp_ids.txt -dir ../data -phenofile phenotypes.txt -outfile allGSK-10-07.ped