impute dosage file confusion

[prabin gurung]

Hi Chris,

I received imputation output from Michigan imputation server (Minimac-4.1.0.2)

Files received: myfile.dose.vcf.gz and myfile.info.gz (screenshots attached; file format: VCF 4.1)

I used the following code to filter out low Rsq and convert to bed/bim/fam format for further downstream analysis:

>plink2 --vcf  myfile.dose.vcf.gz dosage=DS --exclude-if-info "R2<=0.8" --make-bed --out myfileFiltered

Query no1:  if we use –make-bed does this keep/retain the dosage info or do we need to use - -make-pgen?

Query no 2: I read from other posts that the genotype dosages has to be on a 0-1 scale  but I see that my vcf file doesn’t have 0-1 scale, So what’s the alternative if not on a 0-1 scale.

I am using  PLINK v2.00a2.3LM 64-bit Intel (24 Jan 2020).

Sorry if the questions sound too naïve, but this is my first time imputing.

Thank you

…..

Lax

[prabin gurung]

A small addition: I am planning to run GWAS 

Thanks

[Christopher Chang]

0. There have been enough bugfixes since Jan 2020 that you probably want to use a newer plink2 build.  The download link for the Jan 2020 build will be removed in a few months.

1. No, you must use --make-pgen if you want to preserve the dosages.

2. DS is expected to be on a 0-2 scale for diploid data.  Your VCF file looks fine.