User: Shicheng Guo
Shicheng Guo • 7.1k
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Posts by Shicheng Guo
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... Only select tag-SNPs and run the relatedness2, the less SNPs you use, the faster it is. ...
written 1 day ago by
Shicheng Guo • 7.1k
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... Simple bi-allelic SNPs without structure: `PLINK`
Coalescent approaches: `GENOME`
Forward-time approaches: `MetaSim` and `simuPop`
Resampling approaches: `Hapgen2`
...
written 1 day ago by
Shicheng Guo • 7.1k
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... Simple bi-allelic SNPs without structure: `PLINK`
Coalescent approaches: `GENOME`
Forward-time approaches: `MetaSim` and `simuPop`
Resampling approaches: `Hapgen2`
...
written 1 day ago by
Shicheng Guo • 7.1k
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... Check the strand and switching just like before to use beagle:
http://faculty.washington.edu/sguy/beagle/strand_switching/strand_switching.html
or try this simple tool:
https://github.com/biocore-ntnu/snpflip
beagle also provide a tool called `conform-gt` https://faculty.washington.edu/browning/ ...
written 1 day ago by
Shicheng Guo • 7.1k
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... Great. Thanks again!! ...
written 3 days ago by
Shicheng Guo • 7.1k
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... It is SNP-heritability, why they don't have twin based heritability. They have have such data, right? ...
written 4 days ago by
Shicheng Guo • 7.1k
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... Nice. Maybe we can thinking about to based a algorithm to weight them and give a prediction ...
written 4 days ago by
Shicheng Guo • 7.1k
0
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... Great question. Waiting for correct answers ...
written 5 days ago by
Shicheng Guo • 7.1k
1
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Answer:
A: compare and merge VCF files
... Suppose you have `chr22.chip` and `chr22.imputation` to be merged. you can try the following way:
plink --bfile chr22.chip --list-duplicate-vars
awk '{print $4}' plink.dupvar | grep -v ID > plink.dupvar.id
plink --bfile chr22.chip --exclude plink.dupvar.id --make-bed --out chr22.c ...
written 6 days ago by
Shicheng Guo • 7.1k
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Answer:
A: Heritability Database
... Heritability of >2,000 traits & disorders in UK Biobank
https://nealelab.github.io/UKBB_ldsc/
...
written 6 days ago by
Shicheng Guo • 7.1k
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