Question

Michigan imputation server quality control failed

1

Entering edit mode

5.8 years ago

Phoenix Mu ▴ 100

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 • 2.7k views

ADD COMMENT • link updated 3.8 years ago by 4galaxy77 2.9k • written 5.8 years ago by Phoenix Mu ▴ 100

1

Entering edit mode

Why did you remove MAF > .5?

ADD REPLY • link 4.6 years ago by curious ▴ 820

score 0 · Answer 1 · 2021-03-23

0

Entering edit mode

3.8 years ago

binodregmi30 ▴ 10

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

ADD COMMENT • link 3.8 years ago by binodregmi30 ▴ 10

0

Entering edit mode

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

ADD REPLY • link 3.8 years ago by 4galaxy77 2.9k