PV2sim

Phenopacket and VCF for simulation

This app creates simulation files for Exomiser to test performance or demonstrate features.

Input files

PV2Sim uses Phenopackets as the basis for simulated cases. The Phenopacket should contain a list of Human Phenotype Ontology terms, a disease diagnosis, and one or two variants deemed to be disease-causing.

PV2Sim needs three input files

The phenopacket (in JSON format)
hp.obo
a template VCF file (usually a file that does not contain a pathogenic variant)

What PV2SIM does

PV2Sim extracts the data from the Phenopacket, and creates an input YAML file for Exomiser. It also extracts the variants from the Phenopacket and spikes them into the VCF file.

Output files

PV2Sim outputs the simulated VCF file (with the disease associated variants) and the YAML file for Exomiser.

Building and running PV2Sim

To build the app, clone this repository and use maven to generate the app.

$ git clone https://github.com/pnrobinson/PV2sim.git
$ cd PV2Sim
$ mvn package

The run the app, enter (at least) the following data.

$ java -jar pv2sim.jar -v template.vcf -p phenopacket.json -h hp.obo

Options

PVSim can adjust the Exomiser parameters (i.e., the settings in the YAML file) with the following flags.

Options:
  -f, --frequency-threshold
    Exomiser frequency threshold
    Default: 0.1
  --help
    display this help message
* -h, --hpo
    path to hp.obo
  -k, --keepNonPatho
    Keep non pathogenic vars (Exomiser)
    Default: true
  -o, --outputContributingVariantsOnly
    output Contributing Variants Only (Exomiser
    Default: false
* -p, --phenopacket
    path to phenopacket
  -x, --prefix
    outputfile prefix
    Default: pv2sim
* -v, --vcf
    path to VCF file
  --vcf-out
    name/path of simulated (output) VCF file
    Default: pv2sim-out.vcf
  -y, --yaml
    path of output YAML file
    Default: pv2sim.yml