Information about ukb23158_500k_OQFE.90pct10dp_qc_variants.txt helper file

• 

  George F UKB Community team Data Analyst

  • 14 March 2025 09:03

  Hi

  The ukb23158_500k_OQFE.90pct10dp_qc_variants.txt file was created the same way as the ukb23145_300k_OQFE.90pct10dp_qc_variants.txt, which was filtered for variants that passed quality control.

  bcftools view -i 'F_PASS(DP>=10 & GT!="mis")> 0.9' -Oz -o <filtered_normVCF> <normVCF>

  Please read: https://dnanexus.gitbook.io/uk-biobank-rap/science-corner/whole-exome-sequencing-oqfe-protocol/generation-and-utilization-of-quality-control-set-90pct10dp-on-oqfe-data/details-on-processing-the-300k-exome-data-to-generate-the-quality-control-set for information about how this file was generated please see

  For best analysis practices please see: https://biobank.ndph.ox.ac.uk/showcase/refer.cgi?id=914

  Hope this helps

  George

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• 

  Dr. Mc. Ninja

  • Edited 21 May 2025 15:12

  From the url provided:

  Alternatively, use the provided helper file named ukb23145_300k_OQFE.90pct10dp_qc_variants.txt, which is a single-column text file containing variants failing the “90pct10dp” depth filter in the CHR:POS:REF:ALT format.

  tldr: ukb23158_500k_OQFE.90pct10dp_qc_variants.txt contains variants that failed quality control!

   

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