Hi Every one 

I am a bit stuck at this error from Michigan Imputation Server, does any one know what this error means and any hint to fix? 
  

> Error: More than 100 obvious strand flips have been detected. Please
> check strand. Imputation cannot be started!

    Statistics: 
    Alternative allele frequency > 0.5 sites: 0
    Reference Overlap: 99.80% 
    Match: 426,485
    Allele switch: 66,772
    Strand flip: 23,263
    Strand flip and allele switch: 13,805
    A/T, C/G genotypes: 642
    Filtered sites: 
    Filter flag set: 0
    Invalid alleles: 0
    Duplicated sites: 286
    NonSNP sites: 0
    Monomorphic sites: 0
    Allele mismatch: 465
    SNPs call rate < 90%: 0


Thanks
beagle provided a java tool called `conform-gt` https://faculty.washington.edu/browning/conform-gt.html

a program for making alleles in a VCF file to be consistent with a reference VCF file, see an example:

```
java -jar conform-gt.24May16.cee.jar gt=input.vcf.gz chrom=$i ref=chr22.1kg.phase3.v5a.EUR.vcf.gz out=output.chr22.beagle.vcf.gz
```

