Gene-based burden test results of loss of function variants (LoFs).
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. This left us with 579 genes with 2+ LoF variants that can be used for the association tests.
We used 2,405 binary phenotypes in the analyses.
We used as inputs the nulls already calculated for GWAS
Tests are performed with regenie --step2 in burden mode using a max mask (i.e. using the maximum number of ALT alleles across sites)