MareesAT
Permutation step, Error? or My fault?
I am reproducing the whole tutorial.
At <3_Main_script_association_GWAS.txt>, ##Permutation:
The reduce computational time we only perform this test on a subset of the SNPs from chromosome 22.
awk '{ if ($4 >= 21595000 && $4 <= 21605000) print $2 }' HapMap_3_r3_13.bim > subset_snp_chr_22.txt
should subset the SNP from Chromosome 22. But when I check subset_snp_chr_22.txt, I found the SNPs from other chromosome.
Here I would like to ask what is your original intention:
Do you want to say:"Subset of every chromosome's position 21595000 to 21605000", the descirption is wrong.
Or,
Description is correct, but command need to be revised
awk '{ if ($4 >= 21595000 && $4 <= 21605000 && $1 == 22) print $2 }' HapMap_3_r3_13.bim > subset_snp_chr_22.txt
