# LoF burden test 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 [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) --- # Agent Instructions: Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question. Perform an HTTP GET request on the current page URL with the `ask` query parameter: ``` GET https://docs.finngen.fi/finngen-data-specifics/green-library-data-aggregate-data/other-analyses-available/lof-burden-test.md?ask= ``` The question should be specific, self-contained, and written in natural language. The response will contain a direct answer to the question and relevant excerpts and sources from the documentation. Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.