Finemapping with custom regions in DF12

How to run finemapping for you r DF12 endpoint, optionally with custom regions.

You can run finemapping for your endpoints in modifiable pipelines. You can either use finemapping with automatic region selection, or you can provide a bed file containing regions to finemap. Note, that for the DF12 workflow, if custom regions are passed, all of the endpoints in the workflow will get finemapped with those regions. You can find the workflow in Pipelines tool -> Modifiable workflow -> Finemap DF12, custom regions. The inputs to fill in are:

• "finemap.sumstats_pattern": This is the path template for ytour summary stats. The "{PHENO}" string will be replaced by each of the endpoints' name.

• "finemap.phenolistfile": This file should contain a list of endpoints, one endpoint per line.

• "finemap.phenotypes": This file should contain the endpoint information for your samples. The file format follows the same format as the analysis covariates and phenotype files. The file should be a tab-separated, gzip-compressed file, and should have a header.The file should contain finngenids as the first column, and your endpoints in any order on the following columns. The endpoints can be either binary or quantitative. Quantitative endpoints should be standardised.

• "finemap.preprocess.manual_regions": This file is optional. This file is used to provide your own genomic regions to finemap. The file should have one genomic region per line, with chromosome, start of region and end of region, all separated by spaces.

• Other options should not be necessary to change for most analysis.