Genotype imputation check

Question

[Sen]

Hi guys,

I want to do some genotype imputation accuracy checks and what I am using is LinkimputeR with vcf inputs. I tried to use bcftools +setGT to add missing values and bcftools gtcheck to check discordance. But it seems something wrong with it, the vcf file added missing value with no discordance with the original one.

Is there any other way to add missing value to vcf for imputation check? In short, is there any standard pipeline for downsampling?

[Sen]

In short, is there any standard pipeline for downsampling? Mod-edit: Moved this content to the top level post.

[Ram]

If you have an update, edit your post and add the content. Or even add a comment. Adding an answer is one of the (if not the) worst ways to do this, so please avoid it in the future. I've fixed your post this time.