Entering edit mode
4.2 years ago
kl
▴
10
Hello,
Does anyone know/have any code to perform GWAS using BOLT-LMM for many phenotypes iteratively in bash so it is more automated, rather than running a GWAS for each phenotype at a time?
Hi Sam,
Thanks for your response. I was wondering if you can also advise on the following if you have used BOLT-LMM. I have a file with hard-called SNPS in .bim,.bed,.fam with my directly genotyped and imputed SNPs combined in these files. For example, chr1.bim has the directly genotyped and the imputed SNPs. For the flag, --modelsnps do we provide the .bim files all over again (they have been through QC before imputation so SNPs of poor quality etc have already been removed)? Do I need to provide files for the following arguments as they are all about dosages? I only had dosages when I downloaded my imputed data from Michigan server but I then converted them to plink format...
I've pasted the code I would use for my data type below. I would really appreciate your advice. Thanks!
Once you convert the file into plink format, you lost the dosage information. As a result of that, you can use the plink file as if you only got the genotype file.
Great thanks. For the --modelSnps file, can I include all the SNPs or would it be best to go into each of my dosage pre-processed chromosome files and include those with a good INFO score?
Filtering will help to remove problematic SNPs, so do try to filter by INFO score first
Is there a way to create a separate job report for each phenotype?
That depends on your job submission system