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.
##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?