GWA_tutorial
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MareesAT
A comprehensive tutorial about GWAS and PRS
Hello - thanks a lot for your efforts, it worked well (tried it in the example datset). Can you please briefly explain what needs to be changed/adapted in the 1st...
Hello, Thank you for your great tutorial. I followed your tutorial step-by-step, but in Population_stratification step, for run Rscript MDS_merged.R, I got an error about can not open MDS_merge2.mds. Actually,...
# Generate a list of FID and IID of the individual(s) with a Pihat above 0.2, to check who had the lower call rate of the pair. # In our...
I have set Rscript.exe in the bin/, When i try to run : $ Rscript --no-save gender_check.R It shows me: The system cannot find the path specified. What should I...
Hi, Thank you for the paper and the step-by-step tutorial! Those are of great help! May I ask a question regarding your paper? It says that the following: > Individuals...
Hi, I found using the current command will result in all variant id specified as "." in the bim file. Is that wrong? Shall we set variant id manually using...
Your paper suggests the following: > For binary traits we suggest to exclude: HWE p value
Respectly MareesAT : When I running the command, plink --vcf ALL.2of4intersection.20100804.genotypes.vcf.gz --make-bed --out ALL.2of4intersection.20100804.genotypes, I have got the work-log below: @----------------------------------------------------------@ | PLINK! | v1.07 | 10/Aug/2009 | |----------------------------------------------------------| |...
While running: ``` # Select autosomal SNPs only (i.e., from chromosomes 1 to 22). awk '{ if ($1 >= 1 && $1
May I ask "For each pair of 'related' individuals with a pihat > 0.2, we recommend to remove the individual with the lowest call rate"? What does call rate mean...
