I am doing imputation with AffyMetrx 5.0 array chip data.
It was quality-controlled, and I am trying (Shapeit2 and Minimac/impute2) and (Michigan Imputation Server),
but keep failing. (Ref. panel: 1000 genome EAS or ASIAN)
I did qc - rs Id - chr and position correction.
The analysis results say:
Allele switch: 50
Strand flip: 47
Strand flip and allele switch: 64
How can I correct Allele Switch or Strand flip into right?