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• How to extract haplotype from Dosage VCF from Michigan Imputation Server? (Eagle phased, minimac imputed)
  I processed a 23andme raw file in the Michigan Imputation Server, it was phased with Eagle and i...
• Minimac3 VCF to .gen and .sample format
  Hi there, I imputed some genotype data using the Michigan imputation server and got the output i...
• Need some help interpreting Michigan Server Imputation output statistics
  Hi all, I have just performed imputation on a chromosome X dataset, using the Michigan Imputation...
• Filter types in the Michigan imputation server output
  Hi all, I have a question about understanding the two filter types from the Michigan imputation ...
• Negative values for imputed genotypes on X chromsomes in females
  Hi there, I imputed a set of around ~10k individuals using the sanger imputation server (1000 Ge...
• GWAS data analysis strategy or pipeline
  Suppose I received 5000 case and 5000 control GWAS study (suppose it is exom-array), what kinds o...
• Step by step instructions to phase with Eagle?
  It’s a little bit convoluted. I just want to impute SNPs in 23andme format like the following: ...
• result of imputation is vice versa
  Dear all, I impute some SNP that I have their real genotype by minimac3. I checked strand alignm...
• How to fix this strand flips for Michigan Imputation Server?
  Hi Every one I am a bit stuck at this error from Michigan Imputation Server, does any one know ...
• Imputation on two genotyping datasets: should I do imputation separately? or merge the two datasets first?
  Hi guys, I'm doing eQTL analysis. The genotyping data are from two sequencing centers using same...
• michigan imputation server
  Hi, I performed imputation on my GWAS data using Michigan imputation server. Now I have two outp...
• How to filter Michigan genotype imputation results
  Hi, I have just downloaded imputation result files from the Michigan Imputation Server. The file...
• Control For Population Stratification In Exome Sequencing Data
  I have next generation exome sequencing data and genotype calls for some case control samples an...
• how to unzip Michigan imputation server output compressed folder
  Hi, I am facing problem to open the compressed Ziped output folder getting from Michigan Imputati...
• Rare variants imputation
  Hi, I am currently working on rare variants association studies from whole genome seq data. I w...
• Phasing And Imputation Using A Combination Of Pedigrees And Population Data
  Through 23andMe, I have SNP genotypes from family members spanning three generations, incl. one p...
• Imputing specific SNPs and merging with original dataset
  I have a query about imputing specific SNPs in genotyping data. I have a small dataset in Plink f...
• Error while running BEAGLE for genotype imputation
  I am trying to run BEAGLE 4.1 for an imputation run. I have core exome chip data on variants of 2...
• Genotype imputation or tagging?
  Hi, I want to evaluate 41 snps in my dataset. However only 19 were genotyped by the plataform (i...
• Does Imputation Always Need Reference Panel
  I've done SNP (6000 SNPs) genotyping of 220 plant varieties using illumina platform, but the file...
• Convert IMPUTE2 to VCF while keeping phase information
  Hi,   I have imputed genotypes using the IMPUTE2 software. Now I need to convert my IMPUTE2 form...