How to fix this strand flips for Michigan Imputation Server?

Question

[Sharon]

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

[1123437586]

Hello, have you solved this error message“Error: More than 100 obvious strand flips have been detected. Please check strand. Imputation cannot be started!”.I am having the same problem now and I hope to get your help. Thank you

[Sharon]

Hello, I used Beagle instead of Michigan Imputation Server and it works with me.

Answer 1

[Shicheng Guo]

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

[Sharon]

Never used beagle. I will check this out and see. Thanks a lot

[anamaria]

Hi,

did you try to use any of those tools and did they work for you? I am having the same problem.

Thanks Ana

[Sharon]

Still trying anamaria. I will post my answer here if it works out.

[anamaria]

thank you, I hope you succeed!

[Sharon]

I used Beagle it self and it works with me with no issues like the server.

[anamaria]

Hi Sharon,

Good to hear that! Can you please post all steps you used to do imputation on Beagle?

Thanks

[ryshi.study]

Hi Guo, I also want to try this command. May I ask where do you find the reference VCF file?