Question: Whats the point of genotype pruning before imputation?
1
gravatar for optimistsso4co3
5 weeks ago by
optimistsso4co310 wrote:

Hey guys,

The point of imputation is to predict un-typed SNPs using D' or r2 values. However, it is standard to remove all SNPs in LD before imputation e.g. with plink command --indep-pairwise. May i ask what's the purpose of removing actually typed SNP's and then trying to "predict them back"? I'm for sure missing something, but still, curiosity is the point of my job heh

edit: I'm following Joni Coleman tutorial (he uses --indep-pairwise to prune and later remove these snp)

ADD COMMENTlink modified 5 weeks ago • written 5 weeks ago by optimistsso4co310
1

Could you provide a link to that protocl:

standard to remove all SNPs in LD before imputation

ADD REPLYlink modified 5 weeks ago • written 5 weeks ago by zx87548.0k

Hey Zack, thanks for response! I’m following John Colemans tutorial https://github.com/JoniColeman/gwas_scripts

ADD REPLYlink written 5 weeks ago by optimistsso4co310
1
gravatar for zx8754
5 weeks ago by
zx87548.0k
London
zx87548.0k wrote:

They are not pruning before imputation, pruning is a step before doing other QC steps, to calculate IBD and remove related individuals, or calculate PCs to remove outlier individuals based on ethnicity. As the final step of QC, there will be plink command something like:

plink --bfile original \
--remove individualsRelated individualsPCoutlier... individualsCallRate ... \
--exclude SNPsHWE... SNPsOtherQC, ... \
--recode oxford \
--out originalQC
ADD COMMENTlink modified 5 weeks ago • written 5 weeks ago by zx87548.0k
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