Question: How to fix this strand flips for Michigan Imputation Server?
4
gravatar for Sharon
12 months ago by
Sharon460
Sharon460 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 • 1.4k views
ADD COMMENTlink modified 12 months ago by Shicheng Guo7.8k • written 12 months ago by Sharon460

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 6 months ago by 11234375860

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

ADD REPLYlink modified 6 months ago • written 6 months ago by Sharon460
4
gravatar for Shicheng Guo
12 months ago by
Shicheng Guo7.8k
Shicheng Guo7.8k 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 3 hours ago • written 12 months ago by Shicheng Guo7.8k

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

ADD REPLYlink written 12 months ago by Sharon460

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 12 months ago by anamaria80

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

ADD REPLYlink written 12 months ago by Sharon460

thank you, I hope you succeed!

ADD REPLYlink written 12 months ago by anamaria80

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

ADD REPLYlink written 11 months ago by Sharon460

Hi Sharon,

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

Thanks

ADD REPLYlink modified 9 months ago • written 9 months ago by anamaria80
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