Extract.md

Extract

This command line splits the lines of the LinearModel command output based on the levels of a category column, and/or extracts specific lines or columns.

Command line

java -Xmx16G -cp your/folder/triogen-X.Y.Z/triogen-X.Y.Z.jar no.uib.triogen.cmd.extract.Extract [parameters]

Note: you need to replace your/folder by the folder where the release is installed, and Z.Y.Z by the version number.

Standard parameters

-h/--help                 Display help text
-v/--version              Display version

Mandatory Parameters

-i/--input                The result file of the [_LinearModel_](cli/LinearModels.md) command.
-o/--out                  Stem of the file where to write the output. Output will be gzipped and indexed.

Additional Parameters

-sv/--split_by_variant    Splits the output creating one file per variant. Default: no split.
-sp/--split_by_pheno      Splits the output creating one file per phenotype. Default: no split.
-col/--columns            The columns containing association summary statistics to include in the results file as comma separated list. Example: cmf.Bc,cmf.Bc.se,cmf.Bc.p. Default: all columns.
-id/--variantId           The ids of the variants to include in the results file as comma separated list. Example: rs123,rs456,rs789. Default: all variants.
-p/--pheno                The phenotypes to include in the results file as comma separated list. Example: pheno1,pheno2,pheno3. Default: all phenotypes.

Command line example

The example below runs extracts the variantId, cmf.Bc.p, cmf.Bm.p, cmf.Bf.p, cmf.h.p, and cmf.intercept.p columns and makes one output file per phenotype. This can typically be used to extract the values necessary to make Manhattan plots.

java -Xmx16G -cp bin/triogen-X.Y.Z/triogen-X.Y.Z.jar no.uib.triogen.cmd.extract.Extract -i myResults.gz -o myResultsTrimmed -c phenotype -v variantId,cmf.Bc.p,cmf.Bm.p,cmf.Bf.p,cmf.h.p,cmf.intercept.p