Michigan Imputation Server does not impute all input files
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4 weeks ago
vtran • 0

Hi,

I recently uploaded 22 vcf.gz files onto the Michigan Imputation Server. The data passed QC and the job ran successfully. However, when I checked the result, there is only 1 imputed file for chromosome 6. Does anyone know why I got this strange result? enter image description here

imputation gwas • 205 views
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Probably related to the warning on the chunks that were removed because of low reference overlap. Is the reference genome (hg19) correct?

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I think so. For the reference panel, I used HapMap 2 (hg19).

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