Finemapping with custom regions in DF12
How to run finemapping for your 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 file defining the regions to finemap for all of your endpoints . You can find the workflow in Pipelines tool -> Modifiable workflow -> FinemapDF12. The inputs to fill in are:
"finemap.sumstats_pattern": This is the path template for your 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.bed_regions_file": This file is optional. This file is used to provide your own genomic regions to finemap, instead of using the automatic region selection. The file should have file paths, one path per line, to the files that specify the custom regions for each endpoint in your workflow. The region files must be in the same order as your phenotypes in the "finemap.phenolistfile". See below for more information about the custom region file format.
Other options should not be necessary to change for most analysis.
Custom region file format
The custom region file is a file that should contain as many lines as there are endpoints in your finemapping job. Each of those lines should contain a google storage file path to the region definition file corresponding to the endpoint on the same line number in phenolistfile. It is very important that the order of endpoints in the phenolistfile is exactly the same as the order of the bed regions file.
For example, if you had two endpoints to finemap, and you wanted to select the regions to finemap, your "finemap.phenolistfile" might look like this:
In that case, your "finemap.bed_regions_file" should look something like this:
Region file format
Each of those region files should be a bed file, that is a file with one genomic region per line. The region format consists of (numeric) chromosome, region start in basepairs, and region end in basepairs, separated with spaces. For example, if you wanted to finemap basepairs 1,000,000-4,000,000 in chromosome 1, and basepairs 55,000,000-57,000,000 in chromosome X, the bed region file for that endpoint would look like the following:
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