Xing to PED Conversion

Posted by on April 15, 2011

Following mallu's request, here is the code I used to convert Xing et al data to Plink's PED format.

#!/bin/bash
dos2unix *.csv
 
head --lines=1  JHS_Genotype.csv > header.txt
awk -F, '{for (i=2;i<=NF;i++) print "0",$i,"0","0","0", "0"}' header.txt > xing.tfam
sed '1d' JHS_Genotype.csv > genotype.csv
sort -t',' -k 1b,1 genotype.csv > genotype_sorted.csv
sort -t',' -k 1b,1 JHS_SNP.csv > snp_sorted.csv
join -t',' -j 1 snp_sorted.csv genotype_sorted.csv > xing_compound.csv
awk -F, '{printf("%s %s 0 %s ",substr($2,4),$1,$3); 
        for (i=6;i<=NF;i++)
                printf("%s %s ",substr($i,1,1),substr($i,2,1));
        printf("\n")}' xing_compound.csv > xing.tped
 
plink --tfile xing --out xing --make-bed --missing-genotype N --output-missing-genotype 0

I make no guarantees that it will work for you. I used it on my Ubuntu box, but I am sure it'll have trouble on Mac OS.

Code, ,

2 Comments.

  1. mallu April 15, 2011 at 7:18 pm

    wow! this is amazing. You are great. please keep on posting such info which will be quite helpful to the newcomers.

  2. sarabjeet April 16, 2011 at 6:57 am

    please also post the code to convert Pan Asian data to plink format. No hurry, when time permits!

    regards,
    sarb