UK BioBank

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2.7 years ago

rogerdavis2609 ▴ 20

Hi,

I have started working on UK Biobank and I am completely clueless about the data structure. Is there is a tutorial (apart from the one provided by UK Biobank) where I can unsderstand the schema better?

Thanks

ukb UK-Biobank GWAS • 1.5k views

ADD COMMENT • link updated 2.7 years ago by Kevin Blighe 87k • written 2.7 years ago by rogerdavis2609 ▴ 20

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How long have you spent on it? Which UK Biobank data have you retrieved?

ADD REPLY • link 2.7 years ago by Kevin Blighe 87k

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Hi Kevin,

Its been more than 2 weeks now, but I am very confused with the data structure. I have a few SNPs and all I want to know for the first instance is how many patients (suppose with lupus) are there that have that SNP in the Biobank. I am very new to GWAS.

ADD REPLY • link 2.7 years ago by rogerdavis2609 ▴ 20

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I see, which supervisor threw you into this deep water? Do you have the PLINK dataset, or the VCF dataset?

ADD REPLY • link 2.7 years ago by Kevin Blighe 87k

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:) ....I have VCF files.

ADD REPLY • link 2.7 years ago by rogerdavis2609 ▴ 20

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I may suggest that you convert the VCF to PLINK format, and then do everything in PLINK. The UK Biobank data should already be available for you in PLINK format, though (?)

PLINK's documentation is excellent, but there will obviously be a learning curve if you are starting from scratch.

ADD REPLY • link 2.7 years ago by Kevin Blighe 87k

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