Question: michigan imputation server
gravatar for Teresa
13 months ago by
United States
Teresa0 wrote:

Hi, I performed imputation on my GWAS data using Michigan imputation server. Now I have two output files: 1).dose.vcf.gz and 2).info.gz

Michigan imputation server use mimimac3 (--format GT,DS,GP) and in the output file ".dose.vcf.gz" are present all the three formats. I'm new on this kind of analysis, so I need some advice to manage and anayze this data.

I used DosageConvertor to convert them into PLINK dosage format using this command:

$DosageConvertor --vcfDose myfile.vcf.gz --info --prefix out_myfile --type plink --format 1

output files: 1) .dosage and 2) .fam.

To perform quality control steps on the imputed data, is this command right?

fcgene --dosage out_myfile.dosage --fam out_myfile.fam --filter-snp crate=0.9,hwe=1e-6,maf=0.05 --filter-indiv crate=0.9 --rsq 0.3 --oformat plink-dosage --out myfile_QC
ADD COMMENTlink modified 13 months ago • written 13 months ago by Teresa0

Have you looked through the manual under 'Chapter 4 - Quality control and format conversion of plink-formatted data'? - see page 20 of

Your filtering criteria per SNP are

  • Call-rate, 90%
  • HWE p value, 0.000001
  • MAF, 5%

Your filtering criteria per sample is:

  • Call-rate, 90%

For the --rsq parameter, you have to take note as it's not what would be typically expected for such a study. The manual states:

Option - -rsq 0.3 will filter those SNPs which have Rsq value smaller or equal to 0.3 and change the format of only those SNPs which have Rsq ≥ 0.3. Rsq is a measure which estimates the squared correlation between imputed and true genotypes

ADD REPLYlink written 13 months ago by Kevin Blighe41k

I would like to work with dosage genotypes rather than hard call genotypes. It is really difficult for me to find a way to obtain a final data with dosage genotypes (calculated in the imputation process performed by Michigan imputation server) and at the same time taking into account QC steps pe- marker and per- individual and the quality of imputation.

It seems that fcgene is able to perform QC steps on dosage data but the option ---rsq does not work on my input file. Rsq is an indicator of the quality of imputation so I think is really important to consider this parameter. But I dont't know how.

Nevertheless, I found a way to work with hard call genotype (even if it is not what I wanted in the first place). Below the code I used:

plink --vcf myfile.dose.vcf.gz --make-bed --double-id --out s1

QC steps using PLINK

plink --bfile file_finale --maf 0.01 --hwe 0.000001 --snps-only --make-bed --out qc1
plink --bfile s1 --bmerge s1 --merge-mode 6
plink --bfile s1 --exclude plink.missnp --make-bed --out s2
plink --bfile s2 --list-duplicate-vars
plink --bfile s2 --exclude plink.dupvar --make-bed --out s3
plink --bfile s3 --qual-scores 7 1 1 --qual-threshold 0.3 --make-bed --out s4
plink --bfile s4 --maf 0.01 --hwe 0.000001 --snps-only --make-bed --out s5
plink --bfile s5 --mind 0.10 --geno 0.10 --make-bed --out FINAL_DATA_QC

Is there a way to perform this steps on the dosage data?

ADD REPLYlink written 13 months ago by Teresa0

Please use ADD COMMENT/ADD REPLY when responding to existing posts to keep threads logically organized.

This comment belongs under @Kevin's answer.

ADD REPLYlink written 13 months ago by genomax65k

Hi Teresa,

I was wondering if you have noticed that there is a discrepancy in the number of variants in the s4.bim file and when it is loaded for the next step to generate s5?

Here is the example:

plink --bfile s3 --qual-scores 7 1 1 --qual-threshold 0.3 --make-bed --out s4

1238706 variants and 7326 people pass filters and QC.
Note: No phenotypes present.
--make-bed to s4.bed + s4.bim + s4.fam ... done.

plink --bfile s4 --maf 0.01 --hwe 0.000001 --snps-only --make-bed --out s5
1133252 variants loaded from .bim file.

I couldn't figure out where are the remaining variants (a total of 105,454). I have tried in 2 other different chromosomes and I noticed the same issue.

Was wondering if anyone had similar issue?

ADD REPLYlink modified 12 months ago by genomax65k • written 12 months ago by lw53710

Hi Teresa, I am interested in if you have found a way to solve the problem with the dosage data.

I wonder what did you do with your DosageConvertor output file? How did you QC on that? Thanks!

ADD REPLYlink written 5 months ago by Molly_K40
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