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Version: 3.26 (unreleased)

Jist

Overview

The Jist tool provides capability to combine multiple Illumina Connected Annotations JSON outputs into one.

How to use

To combine the JSON outputs, make sure the Jasix index files (.jsi) are presented along with the json files. If the Jasix index file is not there, use Jasix to generate before runing Jist.

Example

dotnet Jist.dll -h
---------------------------------------------------------------------------
Jist                                                (c) 2024 Illumina, Inc.
                                                                     3.25.0
---------------------------------------------------------------------------

USAGE: dotnet Jist.dll -i /path/to/nirvana/output/prefix -o /path/to/combined/json
Combines multiple Illumina Connected Annotations JSON files into one

OPTIONS:
      --in, -i <VALUE>       input file prefix
      --out, -o <VALUE>      compressed output file name (default:console)
      --help, -h             displays the help menu
      --version, -v          displays the version

##### Supported Annotation Sources #####
Basic Tier: DECIPHER, GME, GERP, DANN, REVEL, ClinGen, gnomAD, phyloP, TOPMed, DGV, 1000 Genomes, CliinVar, dbSNP, FusionCatcher, MITOMAP, MultiZ100Way

Professional Tier: PrimateAI(GRCh37), PrimateAI-3D(GRCh38), SpliceAI, COSMIC, OMIM.

##### Contact #####
Professional content licensing, feedback and technical support: annotation_support@illumina.com.
dotnet Jist.dll -i input/Dragen-VC-wg_somatic_tumor_normal -o output/Dragen-VC-wg_somatic_tumor_normal_combined.json.gz
---------------------------------------------------------------------------
Jist                                                (c) 2024 Illumina, Inc.
                                                                     3.25.0
---------------------------------------------------------------------------

Files to stitch
input/Dragen-VC-wg_somatic_tumor_normal-chr1-hg38.json.gz
input/Dragen-VC-wg_somatic_tumor_normal-chr2-hg38.json.gz
input/Dragen-VC-wg_somatic_tumor_normal-chr3-hg38.json.gz
Total position blocks written: 231
Gene lines read: 1368
Unique gene lines: 588

Time: 00:00:00.1