Jasix

Overview

The Jasix index is aimed at providing TABIX like indexing capabilities for the Illumina Connected Annotations JSON output.

Creating the Jasix index

The Jasix index (that comes in a .jsi) file is generated on-the-fly with Illumina Connected Annotations output. It can also be generated independently by running the Jasix command line utility on the JSON output file. Please note that the Jasix utility can only consume JSON files that follow the Illumina Connected Annotations JSON output format. The following code blocks demonstrate the help menu and index generating functionalities of Jasix.

Example

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 <VALUE>       input
      --out, -o <VALUE>      compressed output file name (default:console)
      --query, -q <VALUE>    query range
      --section, -s <VALUE>  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: [e-mail].

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.

dotnet Jasix.dll -i input.json.gz chrM:5000-7000

{
   "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).

dotnet Jasix.dll -i input.json.gz  -q chrM:5000-7000 -q chrM:8500-9500 -t

{
   "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 Illumina Connected Annotations JSON file has three sections: header, positions and genes. Header can be printed using the -H option. If you are interested in only the positions or genes section, you can use the -s or --section option.

dotnet Jasix.dll -i input.json.gz  -s genes

[
{
  "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"
          ]
        }
      ]
    }
  ]
}
]