# 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](https://github.com/FINNGEN/LOFanalysis).

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)