User: Sharon
Sharon • 470
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Posts by Sharon
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Comment:
C: GT 2/3, or 3/3 or 2/2 in vcf
... Hi Tania
I think I understand your question. I think you assume that the reference is the first entry and this confuses you that you assume GT should be 0/1 or 1/1 or 1/2 or 1/3 etc like the first one is usually 0 or 1? Right? Because I was there too :)
These are indeces so in Devon answer 0 is ...
written 4 weeks ago by
Sharon • 470
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... Hello, I used Beagle instead of Michigan Imputation Server and it works with me. ...
written 12 months ago by
Sharon • 470
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... Great, thank you :) ...
written 13 months ago by
Sharon • 470
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... Yes, I realised that also. Thanks Kevin :) ...
written 13 months ago by
Sharon • 470
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... I used Beagle it self and it works with me with no issues like the server. ...
written 17 months ago by
Sharon • 470
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... Still trying anamaria. I will post my answer here if it works out. ...
written 18 months ago by
Sharon • 470
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... Never used beagle. I will check this out and see. Thanks a lot ...
written 18 months ago by
Sharon • 470
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... 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:
Alternativ ...
written 18 months ago by
Sharon • 470
• updated
18 months ago by
Shicheng Guo • 8.2k
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... Good catch. I should use Ghr37, I will check if this will remove the duplications. Thanks Kevin a lot. Always helpful. ...
written 18 months ago by
Sharon • 470
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... **Hi Everyone**
I am trying to use Michigan Impute Server. I use Checkvcf first to avoid failure in the server.
python checkVCF.py -r checkVCF/hs37d5.fa -o test chr3.vcf
**I got some duplicates and inconsistent ref.**
> checkVCF.py -- check validity of VCF file for meta-analysis v ...
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