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LocusZoom.md

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LocusZoom

This command extracts the data needed to make locus zoom plots from the results of the LinearModel command in text tables.

General considerations

Files need to be formatted as detailed here.

A connection to the Ensembl API must be available for gene mapping.

Command line

java -Xmx16G -cp your/folder/triogen-X.Y.Z/triogen-X.Y.Z.jar no.uib.triogen.cmd.locus.LocusZoom [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

-res/results              The results file of the [_LinearModel_](LinearModel.md) command.
-l/--ldMatrix             The LD matrix file as generated using the [_LdMatrix_](LdMatrix.md) command. If LD matrix files are computed per chromosome, replace the chromosome name with '{contig}'.
-f/--fam                  The trio identifiers file.
-vi/--variantId           File listing the variants to query.
-o/--out                  The file where to write the data needed to build a locus zoom plot.

Additional Parameters

-pn/--phenoName           The name of the phenotype to export the locus zoom data on. Example: pheno1. Default: all phenotypes found for the given variants.
-d/--dist                 The maximum distance in bp to consider around a variant. Should be below the distance used to create the ld matrix and, if gene mapping is conducted, below 2.5e6. Default: 1000000.
-g/--geneCoordinates      The file where to write the gene coordinates. If none provided gene mapping will be skipped.
-b/--buildNumber          The number of the build to use if gene mapping is conducted. e.g. 38 for GRCh38. Default: 38.
-log/--log                The file where to write the log. Default: next to the output.

Processing

For each phenotype, variants are selected from lowest p-values until reaching maxP excluding variants with an LD R2 >= minR2 with any of the already selected variants.

Output

The entire lines of the variants passing the pruning are written to the output as they were in the input.