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Oncogenic Results of Analyzing the Genome

Orange summarizes the key outputs from all algorithms in the Hartwig suite into a single PDF and JSON file.

Example report for a whole genome sample.

Example report for a targeted panel sample.

Orange User Manual

Command

Orange uses most outputs from the WiGiTs pipeline.

WGS mode

java -jar orange.jar \
    -experiment_type "PANEL"
    -tumor TUMOR_ID \
    -reference REFERENCE_ID \
    -primary_tumor_location Skin \
    -ref_genome_version V38 \
    -pipeline_sample_root_dir /sample_oa_results/
    -output_dir /path/to/where/to/write/output \

Targeted Panel mode

java -jar orange.jar \
    -experiment_type "PANEL"
    -tumor TUMOR_ID \
    -panel_name "TSO500"
    -primary_tumor_location Skin \
    -pipeline_sample_root_dir /sample_oa_results/
    -output_dir /path/to/where/to/write/output \

Arguments

Argument Description
pipeline_version_file Path to the file containing the (platinum) pipeline version used.
sampling_date Sets the sampling date to the specified date if set. Expected format is YYMMDD. If omitted, current date is used as sampling date.
sequencing_type Illumina (default), SBX, Ultima
ref_genome_version V37 (default) or V38
primary_tumor_location Printed at top of report
experiment_type WGS or PANEL
rna_sample_id Used to display RNA sample genotype values from SageAppend
panel_name Optional, for display only
add_disclaimer If set, adds a "research use only" disclaimer to the footer of every page.
pipeline_sample_root_dir Optional, all individual algo paths are derived from this path, assuming the pipeline has been run using HMF pipeline
sample_data_dir Optional, all data is expected to exist in the root of this path