Closed:How can I analyze the data provided by Michigan Imputation server using ProbABEL?

Question

[sanjana.sundaresan]

Hello!

I'm very new to GWAS and I'm performing imputation for the first time. Please help me out here! Thanks! Forgive me if this has been addressed previously. If so, please provide me with the link.

I've imputed my data using the Michigan Imputation Server which uses the minimac3 software. The output has two files: chr#.info and chr#.dose.vcf. I would like to run the analysis using ProbABEL as it supports minimac and MaCH. I have the following questions:

1. Will I be able to run an analysis with the provided files? I don't seem to have a file with the phenotype of interest and the covariates.

2. The info file format has the columns:

   SNP    REF(0)    ALT(1)    ALT_Frq    MAF    AvgCall    Rsq    Genotyped    LooRsq    EmpR    EmpRsq    Dose0    Dose1
   1:10177    A    AC    0.43686    0.43686    0.58041    0.01965    Imputed    -    -    -    -    -
   1:10235    T    TA    0.00106    0.00106    0.99894    0.00005    Imputed    -    -    -    -    -
   1:10352    T    TA    0.44435    0.44435    0.57366    0.01838    Imputed    -    -    -    -    -
   

   How would I be able to use this file to run an analysis using ProbABEL? If yes, how should it be modified.

3. The dosage file is in vcf format and looks nothing like the MLDOSE file that is required.

   ##fileformat=VCFv4.1
   ##filedate=2016.1.19
   ##source=Minimac3
   ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
   ##FORMAT=<ID=DS,Number=1,Type=Float,Description="Estimated Alternate Allele Dosage : [P(0/1)+2*P(1/1)]">
   ##FORMAT=<ID=GP,Number=3,Type=Float,Description="Estimated Posterior Probabilities for Genotypes 0/0, 0/1 and 1/1 ">
   ##INFO=<ID=MAF,Number=1,Type=Float,Description="Estimated Alternate Allele Frequency">
   ##INFO=<ID=R2,Number=1,Type=Float,Description="Estimated Imputation Accuracy">
   ##INFO=<ID=ER2,Number=1,Type=Float,Description="Empirical (Leave-One-Out) R-square (available only for genotyped variants)">
   #CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT
   

   How should I proceed?

4. How else can I analyze the data? Is there a different program that would suit my data and I can use to analyze?

Thanks!