> For the complete documentation index, see [llms.txt](https://help.bioinsight.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.bioinsight.illumina.com/annotation/utilities/jasix.md). # Jasix ### Overview The Jasix index provides TABIX-like indexing capabilities for DRAGEN Annotation JSON output. ### Creating the Jasix index The Jasix index file (`.jsi`) is generated on the fly with DRAGEN Annotation output. You can also generate it by running the Jasix command-line utility on a JSON output file. Jasix only consumes JSON files that follow the DRAGEN Annotation JSON output format. The following code blocks demonstrate the help menu and index generation. #### Example ```scss dotnet Jasix.dll -h USAGE: dotnet Jasix.dll -i in.json.gz [options] Indexes a Illumina Connected Annotations annotated JSON file OPTIONS: --header, -t print also the header lines --only-header, -H print only the header lines --list, -l list chromosome and section names --index, -c create index --in, -i input --out, -o compressed output file name (default:console) --query, -q query range --section, -s complete section (positions or genes) to output --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. ``` ```scss dotnet Jasix.dll --index -i input.json.gz --------------------------------------------------------------------------- Jasix (c) 2024 Illumina, Inc. 3.25.0 --------------------------------------------------------------------------- Ref Sequence chrM indexed in 00:00:00.2 Ref Sequence chr1 indexed in 00:00:05.8 Ref Sequence chr2 indexed in 00:00:06.0 . . . Peak memory usage: 28.5 MB Time: 00:01:14.8 ``` ### Querying the index The Jasix query format is chr:start-end. If not provided, it assumes end=start. If only chr is provided, all entries for that chromosome will be provided. ```scss dotnet Jasix.dll -i input.json.gz chrM:5000-7000 ``` ```json { "positions":[ { "chromosome":"chrM", "refAllele":"C", "position":5581, "quality":3070.00, "filters":[ "LowGQXHomSNP" ], "altAlleles":[ "T" ], "samples":[ { "variantFreq":1, "totalDepth":1625, "genotypeQuality":1, "alleleDepths":[ 0, 1625 ], "genotype":"1/1" } ], "variants":[ { "altAllele":"T", "refAllele":"C", "begin":5581, "chromosome":"chrM", "end":5581, "variantType":"SNV", "vid":"MT:5581:T" } ] }, { "chromosome":"chrM", "refAllele":"A", "position":6267, "quality":1637.00, "filters":[ "LowGQXHetSNP" ], "altAlleles":[ "G" ], "samples":[ { "variantFreq":0.6873, "totalDepth":323, "genotypeQuality":1, "alleleDepths":[ 101, 222 ], "genotype":"0/1" } ], "variants":[ { "altAllele":"G", "refAllele":"A", "begin":6267, "chromosome":"chrM", "end":6267, "variantType":"SNV", "vid":"MT:6267:G" } ] } ] } ``` The default output stream is Console. However, if an output filename is provided, Jasix outputs the results to that file in a bgzip compressed format. The output is always a valid JSON entry. If requested (via -t option) the header of the indexed file will be provided. Multiple queries can be submitted in the same command and the output will contain them within the same "positions" block in order of the submitted queries (Warning: if the queries are out of order, or overlapping, the output will be out or order and intersecting). ```scss dotnet Jasix.dll -i input.json.gz -q chrM:5000-7000 -q chrM:8500-9500 -t ``` ```json { "header":{ "annotator":"Illumina Annotation Engine 1.6.2.0", "creationTime":"2017-08-30 11:42:57", "genomeAssembly":"GRCh37", "schemaVersion":6, "dataVersion":"84.24.39", "dataSources":[ { "name":"VEP", "version":"84", "description":"Ensembl", "releaseDate":"2017-01-16" } ], "samples":[ "Mother" ] }, "positions":[ { "chromosome":"chrM", "refAllele":"C", "position":5581, "quality":3070.00, "filters":[ "LowGQXHomSNP" ], "altAlleles":[ "T" ], "samples":[ { "variantFreq":1, "totalDepth":1625, "genotypeQuality":1, "alleleDepths":[ 0, 1625 ], "genotype":"1/1" } ], "variants":[ { "altAllele":"T", "refAllele":"C", "begin":5581, "chromosome":"chrM", "end":5581, "variantType":"SNV", "vid":"MT:5581:T" } ] }, { "chromosome":"chrM", "refAllele":"A", "position":6267, "quality":1637.00, "filters":[ "LowGQXHetSNP" ], "altAlleles":[ "G" ], "samples":[ { "variantFreq":0.6873, "totalDepth":323, "genotypeQuality":1, "alleleDepths":[ 101, 222 ], "genotype":"0/1" } ], "variants":[ { "altAllele":"G", "refAllele":"A", "begin":6267, "chromosome":"chrM", "end":6267, "variantType":"SNV", "vid":"MT:6267:G" } ] }, { "chromosome":"chrM", "refAllele":"G", "position":8702, "quality":3070.00, "filters":[ "LowGQXHomSNP" ], "altAlleles":[ "A" ], "samples":[ { "variantFreq":0.9987, "totalDepth":1534, "genotypeQuality":1, "alleleDepths":[ 2, 1532 ], "genotype":"1/1" } ], "variants":[ { "altAllele":"A", "refAllele":"G", "begin":8702, "chromosome":"chrM", "end":8702, "variantType":"SNV", "vid":"MT:8702:A" } ] }, { "chromosome":"chrM", "refAllele":"G", "position":9378, "quality":3070.00, "filters":[ "LowGQXHomSNP" ], "altAlleles":[ "A" ], "samples":[ { "variantFreq":1, "totalDepth":1018, "genotypeQuality":1, "alleleDepths":[ 0, 1018 ], "genotype":"1/1" } ], "variants":[ { "altAllele":"A", "refAllele":"G", "begin":9378, "chromosome":"chrM", "end":9378, "variantType":"SNV", "vid":"MT:9378:A" } ] } ] } ``` ### Extracting a section The DRAGEN Annotation JSON file has three sections: header, positions, and genes. Print the header with `-H`. To select only positions or genes, use `-s` or `--section`. ```scss dotnet Jasix.dll -i input.json.gz -s genes ``` ```json [ { "name": "ABCB10", "omim": [ { "mimNumber": 605454, "geneName": "ATP-binding cassette, subfamily B, member 10" } ] }, { "name": "ABCD3", "omim": [ { "mimNumber": 170995, "geneName": "ATP-binding cassette, subfamily D, member 3 (peroxisomal membrane protein 1, 70kD)", "description": "The ABCD3 gene encodes a peroxisomal membrane transporter involved in the transport of branched-chain fatty acids and C27 bile acids into the peroxisome; the latter function is a crucial step in bile acid biosynthesis (summary by Ferdinandusse et al., 2015).", "phenotypes": [ { "mimNumber": 616278, "phenotype": "?Bile acid synthesis defect, congenital, 5", "mapping": "molecular basis of the disorder is known", "inheritances": [ "Autosomal recessive" ], "comments": [ "unconfirmed or possibly spurious mapping" ] } ] } ] } ] ``` --- # Agent Instructions This documentation is published with GitBook. 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