LoF burden test

Loss of function (LoF) variants were generated from vcf files with VEP (https://github.com/Ensembl/ensembl-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 github.

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)