User: Sharon

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Sharon470
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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 Sharon470
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Comment: C: How to fix this strand flips for Michigan Imputation Server?
... Hello, I used Beagle instead of Michigan Imputation Server and it works with me. ...
written 12 months ago by Sharon470
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Comment: C: Relatedness vs relatedness2 from vcftools give different results
... Great, thank you :) ...
written 13 months ago by Sharon470
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Comment: C: Annovar for mouse buildver and downdb?
... Yes, I realised that also. Thanks Kevin :) ...
written 13 months ago by Sharon470
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Comment: C: How to fix this strand flips for Michigan Imputation Server?
... I used Beagle it self and it works with me with no issues like the server. ...
written 17 months ago by Sharon470
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Comment: C: How to fix this strand flips for Michigan Imputation Server?
... Still trying anamaria. I will post my answer here if it works out. ...
written 18 months ago by Sharon470
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Comment: C: How to fix this strand flips for Michigan Imputation Server?
... Never used beagle. I will check this out and see. Thanks a lot ...
written 18 months ago by Sharon470
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How to fix this strand flips for Michigan Imputation Server?
... 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 ...
imputation snp written 18 months ago by Sharon470 • updated 18 months ago by Shicheng Guo8.2k
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Comment: C: How to remove duplicate sites and inconsistent sites from a VCF?
... 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 Sharon470
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How to remove duplicate sites and inconsistent sites from a VCF?
... **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 ...
vcf michigan impute server plink written 18 months ago by Sharon470 • updated 16 months ago by Biostar ♦♦ 20

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