ukb23145_300k_OQFE.sets.txt.gz
ukb23145_300k_OQFE.annotations.txt.gz
ukb23145_300k_OQFE.masks
--aaf-bins
to specify AAF cutoffs to use when building masks (the singleton class of masks is always included)--aaf-bins 0.05,0.01
` will build masks using singletons, 1% and 5% AAF cutoffs.--ignore-pred
to bypass specifying the LOCO PRS. --extract-setlist
to specify a subset of the 19K genes to test. Alternatively, you can provide a file named like extract_gene_names.txt, with a single column containing names of genes to analyze, then pass this file to regenie using --extract-sets extract_gene_names.txt
:--write-mask
, which will store the masks in PLINK BED format, in files ldl_pcsk9_test_masks.{bed,bim,fam}.--skip-test
.--build-mask sum
will take the sum of the ALT allele count across sites--build-mask comphet
is used to identify compound heterozygotes, which is defined as carriers of 2 or more ALT alleles across any site included in the mask --write-mask
as detailed above.--write-mask-snplist
when building masks. This will generate a file where each row has the mask name followed by the list of variants that went into the mask.--check-burden-files
, which will create a report that checks the input files for concordance. It will check that the same annotation labels are used in all files, and check that there are variants in the set list file which are not in the input genotype file.--mask-lovo
followed by the gene name, the mask name, and the AAF cutoff (either 'singleton' or a value in (0,1)).