LoF burden test
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Loss of function (LoF) variants were generated from vcf files with VEP (). LoF variants are defined as having consequences in the list [frameshift_variant,splice_donor_variant,stop_gained,splice_acceptor_variant]. Also, a max_maf (0.01) and minimum info score (0.8) filters are applied. Then a bgen file is formed by filtering chromosome based vcfs and merging them into a single file, allowing us to run the whole analysis in one data set. Then the bgen is passed to step 2 of regenie in burden mode, which uses the nulls from the standard GWAS runs.
More detailed description of the pipeline used to create the results can be found in .
Results for lof burden test for for example DF11 can be found from: /finngen/library-green/finngen_R11/finngen_R11_analysis_data/lof/data
(NOTE: lof burden test has NOT been run for releases 9 and 7)