UK biobank exome filtering

Question

[Floris Brenk]

Dear all,

Was wondering whether anyone already figured out how to filter the UKBiobank 200K exome data? The paper describes this:

"Variants that passed the following criteria are included: individual and variant missingness 10^-15, minimum read coverage depth of 7 for SNPs and 10 for indels, at least one sample per site passed the allele balance threshold > 0.15 for SNPs and 0.20 for indels."

Given that the data is ~8TB, was wondering whether anyone knows a cost-effective and efficient way of filtering the pvcf files for this... looking into bcftools but not sure it can do all these steps.

Thanks!

[Scott]

One easy but far from perfect QC solution is to use the variants included in the FE pipeline. The pipeline is described in the last paragraph of https://biobank.ndph.ox.ac.uk/ukb/label.cgi?id=170, and the FE bim file https://biobank.ndph.ox.ac.uk/ukb/refer.cgi?id=1534. Just filter to those variants.