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miguelpmachado/exomizer

By miguelpmachado

•Updated over 6 years ago

A Tool to Annotate and Prioritize Exome Variants

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242

miguelpmachado/exomizer repository overview

⁠Exomiser

Docker image for Exomizer GitHub⁠ (extra links: link_1⁠, link_2⁠, link_3⁠, The Monarch Initiative⁠)

A Tool to Annotate and Prioritize Exome Variants.

The Exomiser is a Java program that finds potential disease-causing variants from whole-exome or whole-genome sequencing data. Starting from a VCF file and a set of phenotypes encoded using the Human Phenotype Ontology (HPO) it will annotate, filter and prioritise likely causative variants. The program does this based on user-defined criteria such as a variant's predicted pathogenicity, frequency of occurrence in a population and also how closely the given phenotype matches the known phenotype of diseased genes from human and model organism data.

Docker file here⁠.

java -Xms2g -Xmx4g -jar exomiser-cli-12.1.0.jar [options]

⁠Important Notes

  • Exomiser data
    • A folder containing the Exomiser data directories (for example, 1909_hg38/ and 1909_phenotype/) should be mapped to container /exomiser_data_directory/ folder.
    • If the data for the different genome versions are in different directories, the /exomiser_data_directory_hg19/ and /exomiser_data_directory_hg38/ folders can be used for hg19 and hg38, respectively.
  • application.properties file
    • A folder containing the customized application.properties file (keeping the same file name, application.properties) should be mapped to container /exomiser_application_properties/ folder.
    • Make sure that all the paths to Exomiser data-directory were changed to the correct mounting points.

Tag summary

Content type

Image

Digest

Size

228.3 MB

Last updated

over 6 years ago

docker pull miguelpmachado/exomizer:12.1.0-01