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• why some genotyped snps are lost after imputation
  Hallo everyone, I'm using IMPUTE2 for genotype data phasing and imputing. But I found that lots ...
• Genotype imputation comparison
  Hello everyone! I need a hand to understand how to perform an imputation performance comparison. ...
• Michigan Imputation Server removed low call rate SNPs
  Hi All, I notice Michigan Imputation Server removed all the low call rate SNPs (rate<90%??) ...
• 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...
• why the Michigan Imputation Server for chrX imputation quality control fails?
  There are only non par in my chrX, when I perform genotype imputation by Michigan Imputation Ser...
• Why does genotype data change after genetic imputation?
  Hello, I am trying to perform genetic imputation on TCGA genotype data so I can perform a GWAS-t...
• Michigan Imputation Server - typed-only sites?
  HI all, I have been trying to carry out imputation on some datasets on the Michigan Imputation Se...
• Minimac3 VCF to .gen and .sample format
  Hi there, I imputed some genotype data using the Michigan imputation server and got the output i...
• Filter types in the Michigan imputation server output
  Hi all, I have a question about understanding the two filter types from the Michigan imputation ...
• 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...
• 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...
• Is there a FASTA file containing 1000 Genomes variant information to check reference alleles in VCF files?
  Hi folks! I've imputed genotype data using the Michigan Imputation Server (MIS), using the 1000 ...
• 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 ...
• Imputing specific SNPs using Beagle5.1
  Hi, I wish to compare the performance of two genotyping chips for phasing and imputation protoco...
• Removing rare variants from SNP array before imputation then putting them back in after imputation?
  I am trying to impute SNP array data on the Michigan imputation server. My overlap with the refer...
• Difference in imputation between platforms and RS names
  Hello, so I have SNPs (RSIDs) from imputation done in 2011 on http://csg.sph.umich.edu/abecasis/...
• 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...
• from phased SNPs to haplotype blocks (or phase sets)
  Hi all, I have successfully **phased a set of heterozygous SNPs** (only one sample) via the **EAG...