Variant from WGS

Sai Prasad Pydi

What is the best approach for identifying genetic variants in RAP WGS data and extracting corresponding subject IDs for phenotypic analysis? I'm new to using the UK Biobank. Is there a step-by-step process outline to proceed?

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    Lea K. Data Analyst The helpers that keep the community running smoothly. UKB Community team
    • Edited

    Hi Sai,

    You can use PLINK to extract genetic variants from WGS data. You may find the SNP extraction notebook useful, it extracts variants from the genotype data. You can do a similar analysis on the WGS data. There are also some command line tools such as bcftools and swiss army knife that are useful, more information can be found in the tools list. Hope this helps.

    Thank you for using the community forum.

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