Michigan imputation server quality control failed

I am using Michigan Imputation Server. I have performed a initial QC and removed monomorphic sites and sites with MAF > 0.5. However, the QC step on the server failed. There is no error message or logfile that I can check.

So I just do not know how to find out what is wrong with my VCF file.

imputation genotype

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updated 5.4 years ago by 4galaxy77

• written 7.4 years ago by Phoenix Mu •

Why did you remove MAF > .5?

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written 6.3 years ago by curious

1 answer

ya! I am also wondering why to remove MAF>0.5?

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written 5.4 years ago by binodregmi30 •

Because it probably means there has been some kind of strand-flip.

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written 5.4 years ago by 4galaxy77

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