PLEASE!!How can I perform association test(GWAS) by using WES data in a pVCF?

Yaying Sun

I want to perform association test by using WES data. However, since the UKB forbids users to download data, I have only found WES data in a pVCF format. I want to firstly do quality control, before which I must have fasta data, but UKB doesn't offer access to it. And I found the link “https://www.ukbiobank.ac.uk/media/najcnoaz/access_064-uk-biobank-exome-release-faq_v11-1_final-002.pdf”. In this PDF, it says that all pVCFs have been finished quality control. But when I want to do next step, the association test, my job failed. The problem is as follows. May be there were still some problems in the VCF. Please can anyone tell me how I can deal with it?

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  • Comment author
    Lucy BG The helpers that keep the community running smoothly. UKB Community team Data Analyst
    • Official comment

    The UK Biobank GitHub has some example code for running a basic ExWAS, and other tutorials for data manipulation ahead of ExWAS or GWAS: https://github.com/UK-Biobank/UKB-RAP-Notebooks

    This may give you a suitable starting point to develop your code for your specific analysis.

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