Question: How to fix this strand flips for Michigan Imputation Server?
5
gravatar for Sharon
2.0 years ago by
Sharon490
Sharon490 wrote:

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

snp imputation • 2.7k views
ADD COMMENTlink modified 2.0 years ago by Shicheng Guo8.5k • written 2.0 years ago by Sharon490

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

ADD REPLYlink written 18 months ago by 11234375860

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

ADD REPLYlink modified 18 months ago • written 18 months ago by Sharon490
5
gravatar for Shicheng Guo
2.0 years ago by
Shicheng Guo8.5k
Shicheng Guo8.5k wrote:

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
ADD COMMENTlink modified 11 months ago • written 2.0 years ago by Shicheng Guo8.5k

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

ADD REPLYlink written 2.0 years ago by Sharon490

Hi,

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

Thanks Ana

ADD REPLYlink written 2.0 years ago by anamaria110

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

ADD REPLYlink written 24 months ago by Sharon490

thank you, I hope you succeed!

ADD REPLYlink written 24 months ago by anamaria110

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

ADD REPLYlink written 23 months ago by Sharon490

Hi Sharon,

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

Thanks

ADD REPLYlink modified 21 months ago • written 21 months ago by anamaria110

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

ADD REPLYlink written 5 weeks ago by ryshi.study10
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