> For the complete documentation index, see [llms.txt](https://help.connected.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.connected.illumina.com/annotation/introduction/parsing-json.md).
# Parsing Illumina Connected Annotations JSON
Our JSON files are organized similarly to original VCF variants:
Illumina Connected Annotations JSON files can get very large and sometimes we receive feedback that a bioinformatician tried to read the JSON file into Python or R resulting in a program that ran out of available RAM. This happens because those parsers try to load everything into memory all at once.
To get around those issues, we play some clever tricks with newlines that enables our users to parse our JSON files quickly and efficiently.
## Organization
Our JSON file is arranged as follows:
* the header section is located on the first line
* each line after that corresponds to a position (same as a row in a VCF file)
* until you reach the genes section `],"genes":[`
* each line after that corresponds to a gene
* until you reach the end `]}`
Knowing this, you can load each position line as an independent JSON object and extract the information you need.
{% hint style="info" %}
**Jupyter Notebook**
To demonstrate this, we have put together a [Jupyter notebook demonstrating how to do this in Python](https://github.com/Illumina/IlluminaConnectedAnnotationsDocumentation/blob/master/static/files/parse-json-python.ipynb) and a [R version](https://github.com/Illumina/IlluminaConnectedAnnotationsDocumentation/blob/master/static/files/parse-json-r.ipynb) as well.
{% endhint %}
## JASIX
One of the tools that we really like in the VCF ecosystem is [tabix](https://dx.doi.org/10.1093%2Fbioinformatics%2Fbtq671). Unfortunately, tabix only works for tab-delimited file formats. As a result, we created a similar tool for Illumina Connected Annotations JSON files called JASIX.
Here's an example of how you might use JASIX:
```bash
dotnet bin/Release/net6.0/Jasix.dll -i dragen.json.gz -q chr1:942450-942455
```
* the `-i` argument specifies the Illumina Connected Annotations JSON path
* the `-q` argument specifies a genomic range *(you can use as many of these as you want)*
JASIX also includes additional options for showing the Illumina Connected Annotations header or for extracting different sections (like the genes section).
The output from JASIX is compliant JSON object shown in pretty-printed form:
```json
{"positions":[
{
"chromosome": "chr1",
"position": 942451,
"refAllele": "T",
"altAlleles": [
"C"
],
"quality": 484.23,
"filters": [
"PASS"
],
"cytogeneticBand": "1p36.33",
"samples": [
{
"genotype": "1/1",
"variantFrequencies": [
1
],
"totalDepth": 21,
"genotypeQuality": 60,
"alleleDepths": [
0,
21
]
},
{
"genotype": "1/1",
"variantFrequencies": [
1
],
"totalDepth": 32,
"genotypeQuality": 93,
"alleleDepths": [
0,
32
]
},
{
"genotype": "1/1",
"variantFrequencies": [
1
],
"totalDepth": 36,
"genotypeQuality": 105,
"alleleDepths": [
0,
36
]
}
],
"variants": [
{
"vid": "1-942451-T-C",
"chromosome": "chr1",
"begin": 942451,
"end": 942451,
"refAllele": "T",
"altAllele": "C",
"variantType": "SNV",
"hgvsg": "NC_000001.11:g.942451T>C",
"phylopScore": -0.1,
"clinvar": [
{
"id": "VCV000836156.1",
"reviewStatus": "criteria provided, single submitter",
"significance": [
"uncertain significance"
],
"refAllele": "T",
"altAllele": "T",
"lastUpdatedDate": "2020-08-20"
},
{
"id": "RCV001037211.1",
"variationId": 836156,
"reviewStatus": "criteria provided, single submitter",
"alleleOrigins": [
"germline"
],
"refAllele": "T",
"altAllele": "T",
"phenotypes": [
"not provided"
],
"medGenIds": [
"CN517202"
],
"significance": [
"uncertain significance"
],
"lastUpdatedDate": "2020-08-20",
"pubMedIds": [
"28492532"
]
}
],
"dbsnp": [
"rs6672356"
],
"gnomad": {
"coverage": 25,
"allAf": 0.999855,
"allAn": 123742,
"allAc": 123724,
"allHc": 61853,
"afrAf": 0.999416,
"afrAn": 10278,
"afrAc": 10272,
"afrHc": 5133,
"amrAf": 0.99995,
"amrAn": 20008,
"amrAc": 20007,
"amrHc": 10003,
"easAf": 1,
"easAn": 6054,
"easAc": 6054,
"easHc": 3027,
"finAf": 1,
"finAn": 8696,
"finAc": 8696,
"finHc": 4348,
"nfeAf": 0.999899,
"nfeAn": 49590,
"nfeAc": 49585,
"nfeHc": 24790,
"asjAf": 1,
"asjAn": 7208,
"asjAc": 7208,
"asjHc": 3604,
"sasAf": 0.99967,
"sasAn": 18160,
"sasAc": 18154,
"sasHc": 9074,
"othAf": 1,
"othAn": 3748,
"othAc": 3748,
"othHc": 1874,
"maleAf": 0.9999,
"maleAn": 69780,
"maleAc": 69773,
"maleHc": 34883,
"femaleAf": 0.999796,
"femaleAn": 53962,
"femaleAc": 53951,
"femaleHc": 26970,
"controlsAllAf": 0.999815,
"controlsAllAn": 48654,
"controlsAllAc": 48645
},
"oneKg": {
"allAf": 1,
"afrAf": 1,
"amrAf": 1,
"easAf": 1,
"eurAf": 1,
"sasAf": 1,
"allAn": 5008,
"afrAn": 1322,
"amrAn": 694,
"easAn": 1008,
"eurAn": 1006,
"sasAn": 978,
"allAc": 5008,
"afrAc": 1322,
"amrAc": 694,
"easAc": 1008,
"eurAc": 1006,
"sasAc": 978
},
"primateAI": [
{
"hgnc": "SAMD11",
"scorePercentile": 0.87
}
],
"revel": {
"score": 0.145
},
"topmed": {
"allAf": 0.999809,
"allAn": 125568,
"allAc": 125544,
"allHc": 62760
},
"transcripts": [
{
"transcript": "ENST00000420190.6",
"source": "Ensembl",
"bioType": "protein_coding",
"geneId": "ENSG00000187634",
"hgnc": "SAMD11",
"consequence": [
"downstream_gene_variant"
],
"proteinId": "ENSP00000411579.2"
},
{
"transcript": "ENST00000342066.7",
"source": "Ensembl",
"bioType": "protein_coding",
"codons": "Tgg/Cgg",
"aminoAcids": "W/R",
"cdnaPos": "1110",
"cdsPos": "1027",
"exons": "10/14",
"proteinPos": "343",
"geneId": "ENSG00000187634",
"hgnc": "SAMD11",
"consequence": [
"missense_variant"
],
"hgvsc": "ENST00000342066.7:c.1027T>C",
"hgvsp": "ENSP00000342313.3:p.(Trp343Arg)",
"polyPhenScore": 0,
"polyPhenPrediction": "benign",
"proteinId": "ENSP00000342313.3",
"siftScore": 1,
"siftPrediction": "tolerated"
},
{
"transcript": "ENST00000618181.4",
"source": "Ensembl",
"bioType": "protein_coding",
"codons": "Tgg/Cgg",
"aminoAcids": "W/R",
"cdnaPos": "732",
"cdsPos": "652",
"exons": "7/11",
"proteinPos": "218",
"geneId": "ENSG00000187634",
"hgnc": "SAMD11",
"consequence": [
"missense_variant"
],
"hgvsc": "ENST00000618181.4:c.652T>C",
"hgvsp": "ENSP00000480870.1:p.(Trp218Arg)",
"polyPhenScore": 0,
"polyPhenPrediction": "benign",
"proteinId": "ENSP00000480870.1",
"siftScore": 1,
"siftPrediction": "tolerated"
},
{
"transcript": "ENST00000622503.4",
"source": "Ensembl",
"bioType": "protein_coding",
"codons": "Tgg/Cgg",
"aminoAcids": "W/R",
"cdnaPos": "1110",
"cdsPos": "1030",
"exons": "10/14",
"proteinPos": "344",
"geneId": "ENSG00000187634",
"hgnc": "SAMD11",
"consequence": [
"missense_variant"
],
"hgvsc": "ENST00000622503.4:c.1030T>C",
"hgvsp": "ENSP00000482138.1:p.(Trp344Arg)",
"isCanonical": true,
"polyPhenScore": 0,
"polyPhenPrediction": "benign",
"proteinId": "ENSP00000482138.1",
"siftScore": 1,
"siftPrediction": "tolerated"
},
{
"transcript": "ENST00000618323.4",
"source": "Ensembl",
"bioType": "protein_coding",
"codons": "cTg/cCg",
"aminoAcids": "L/P",
"cdnaPos": "712",
"cdsPos": "632",
"exons": "8/12",
"proteinPos": "211",
"geneId": "ENSG00000187634",
"hgnc": "SAMD11",
"consequence": [
"missense_variant"
],
"hgvsc": "ENST00000618323.4:c.632T>C",
"hgvsp": "ENSP00000480678.1:p.(Leu211Pro)",
"polyPhenScore": 0,
"polyPhenPrediction": "unknown",
"proteinId": "ENSP00000480678.1",
"siftScore": 0.03,
"siftPrediction": "deleterious - low confidence"
},
{
"transcript": "ENST00000616016.4",
"source": "Ensembl",
"bioType": "protein_coding",
"codons": "ccT/ccC",
"aminoAcids": "P",
"cdnaPos": "944",
"cdsPos": "864",
"exons": "9/13",
"proteinPos": "288",
"geneId": "ENSG00000187634",
"hgnc": "SAMD11",
"consequence": [
"synonymous_variant"
],
"hgvsc": "ENST00000616016.4:c.864T>C",
"hgvsp": "ENST00000616016.4:c.864T>C(p.(Pro288=))",
"proteinId": "ENSP00000478421.1"
},
{
"transcript": "ENST00000618779.4",
"source": "Ensembl",
"bioType": "protein_coding",
"codons": "Tgg/Cgg",
"aminoAcids": "W/R",
"cdnaPos": "921",
"cdsPos": "841",
"exons": "9/13",
"proteinPos": "281",
"geneId": "ENSG00000187634",
"hgnc": "SAMD11",
"consequence": [
"missense_variant"
],
"hgvsc": "ENST00000618779.4:c.841T>C",
"hgvsp": "ENSP00000484256.1:p.(Trp281Arg)",
"polyPhenScore": 0,
"polyPhenPrediction": "benign",
"proteinId": "ENSP00000484256.1",
"siftScore": 1,
"siftPrediction": "tolerated"
},
{
"transcript": "ENST00000616125.4",
"source": "Ensembl",
"bioType": "protein_coding",
"codons": "Tgg/Cgg",
"aminoAcids": "W/R",
"cdnaPos": "783",
"cdsPos": "703",
"exons": "8/12",
"proteinPos": "235",
"geneId": "ENSG00000187634",
"hgnc": "SAMD11",
"consequence": [
"missense_variant"
],
"hgvsc": "ENST00000616125.4:c.703T>C",
"hgvsp": "ENSP00000484643.1:p.(Trp235Arg)",
"polyPhenScore": 0,
"polyPhenPrediction": "benign",
"proteinId": "ENSP00000484643.1",
"siftScore": 1,
"siftPrediction": "tolerated"
},
{
"transcript": "ENST00000620200.4",
"source": "Ensembl",
"bioType": "protein_coding",
"codons": "cTg/cCg",
"aminoAcids": "L/P",
"cdnaPos": "427",
"cdsPos": "347",
"exons": "5/9",
"proteinPos": "116",
"geneId": "ENSG00000187634",
"hgnc": "SAMD11",
"consequence": [
"missense_variant"
],
"hgvsc": "ENST00000620200.4:c.347T>C",
"hgvsp": "ENSP00000484820.1:p.(Leu116Pro)",
"polyPhenScore": 0,
"polyPhenPrediction": "unknown",
"proteinId": "ENSP00000484820.1",
"siftScore": 0.16,
"siftPrediction": "tolerated - low confidence"
},
{
"transcript": "ENST00000617307.4",
"source": "Ensembl",
"bioType": "protein_coding",
"codons": "Tgg/Cgg",
"aminoAcids": "W/R",
"cdnaPos": "867",
"cdsPos": "787",
"exons": "9/13",
"proteinPos": "263",
"geneId": "ENSG00000187634",
"hgnc": "SAMD11",
"consequence": [
"missense_variant"
],
"hgvsc": "ENST00000617307.4:c.787T>C",
"hgvsp": "ENSP00000482090.1:p.(Trp263Arg)",
"polyPhenScore": 0,
"polyPhenPrediction": "benign",
"proteinId": "ENSP00000482090.1",
"siftScore": 1,
"siftPrediction": "tolerated"
},
{
"transcript": "NM_152486.2",
"source": "RefSeq",
"bioType": "protein_coding",
"codons": "Cgg/Cgg",
"aminoAcids": "R",
"cdnaPos": "1107",
"cdsPos": "1027",
"exons": "10/14",
"proteinPos": "343",
"geneId": "148398",
"hgnc": "SAMD11",
"consequence": [
"synonymous_variant"
],
"hgvsc": "NM_152486.2:c.1027T>C",
"hgvsp": "NM_152486.2:c.1027T>C(p.(Arg343=))",
"isCanonical": true,
"proteinId": "NP_689699.2"
},
{
"transcript": "ENST00000341065.8",
"source": "Ensembl",
"bioType": "protein_coding",
"codons": "Tgg/Cgg",
"aminoAcids": "W/R",
"cdnaPos": "750",
"cdsPos": "751",
"exons": "8/12",
"proteinPos": "251",
"geneId": "ENSG00000187634",
"hgnc": "SAMD11",
"consequence": [
"missense_variant"
],
"hgvsc": "ENST00000341065.8:c.750T>C",
"hgvsp": "ENSP00000349216.4:p.(Trp251Arg)",
"polyPhenScore": 0,
"polyPhenPrediction": "benign",
"proteinId": "ENSP00000349216.4",
"siftScore": 1,
"siftPrediction": "tolerated"
},
{
"transcript": "ENST00000455979.1",
"source": "Ensembl",
"bioType": "protein_coding",
"codons": "Tgg/Cgg",
"aminoAcids": "W/R",
"cdnaPos": "507",
"cdsPos": "508",
"exons": "4/7",
"proteinPos": "170",
"geneId": "ENSG00000187634",
"hgnc": "SAMD11",
"consequence": [
"missense_variant"
],
"hgvsc": "ENST00000455979.1:c.507T>C",
"hgvsp": "ENSP00000412228.1:p.(Trp170Arg)",
"polyPhenScore": 0,
"polyPhenPrediction": "benign",
"proteinId": "ENSP00000412228.1",
"siftScore": 1,
"siftPrediction": "tolerated"
},
{
"transcript": "ENST00000478729.1",
"source": "Ensembl",
"bioType": "processed_transcript",
"geneId": "ENSG00000187634",
"hgnc": "SAMD11",
"consequence": [
"downstream_gene_variant"
]
},
{
"transcript": "ENST00000474461.1",
"source": "Ensembl",
"bioType": "retained_intron",
"cdnaPos": "389",
"exons": "3/4",
"geneId": "ENSG00000187634",
"hgnc": "SAMD11",
"consequence": [
"non_coding_transcript_exon_variant"
],
"hgvsc": "ENST00000474461.1:n.389T>C"
},
{
"transcript": "ENST00000466827.1",
"source": "Ensembl",
"bioType": "retained_intron",
"cdnaPos": "191",
"exons": "2/2",
"geneId": "ENSG00000187634",
"hgnc": "SAMD11",
"consequence": [
"non_coding_transcript_exon_variant"
],
"hgvsc": "ENST00000466827.1:n.191T>C"
},
{
"transcript": "ENST00000464948.1",
"source": "Ensembl",
"bioType": "retained_intron",
"cdnaPos": "286",
"exons": "1/2",
"geneId": "ENSG00000187634",
"hgnc": "SAMD11",
"consequence": [
"non_coding_transcript_exon_variant"
],
"hgvsc": "ENST00000464948.1:n.286T>C"
},
{
"transcript": "NM_015658.3",
"source": "RefSeq",
"bioType": "protein_coding",
"geneId": "26155",
"hgnc": "NOC2L",
"consequence": [
"downstream_gene_variant"
],
"isCanonical": true,
"proteinId": "NP_056473.2"
},
{
"transcript": "ENST00000483767.5",
"source": "Ensembl",
"bioType": "retained_intron",
"geneId": "ENSG00000188976",
"hgnc": "NOC2L",
"consequence": [
"downstream_gene_variant"
]
},
{
"transcript": "ENST00000327044.6",
"source": "Ensembl",
"bioType": "protein_coding",
"geneId": "ENSG00000188976",
"hgnc": "NOC2L",
"consequence": [
"downstream_gene_variant"
],
"isCanonical": true,
"proteinId": "ENSP00000317992.6"
},
{
"transcript": "ENST00000477976.5",
"source": "Ensembl",
"bioType": "retained_intron",
"geneId": "ENSG00000188976",
"hgnc": "NOC2L",
"consequence": [
"downstream_gene_variant"
]
},
{
"transcript": "ENST00000496938.1",
"source": "Ensembl",
"bioType": "processed_transcript",
"geneId": "ENSG00000188976",
"hgnc": "NOC2L",
"consequence": [
"downstream_gene_variant"
]
}
]
}
]
}
]}
```
---
# Agent Instructions
This documentation is published with GitBook. GitBook is the documentation platform designed so that both humans and AI agents can read, navigate, and reason over technical content effectively. Learn more at gitbook.com.
## Querying This Documentation
If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question.
Perform an HTTP GET request on the current page URL with the `ask` query parameter, and the optional `goal` query parameter:
```
GET https://help.connected.illumina.com/annotation/introduction/parsing-json.md?ask=&goal=
```
`ask` is the immediate question: it should be specific, self-contained, and written in natural language.
`goal` is optional and describes the broader end goal you are ultimately trying to accomplish on behalf of the user. GitBook uses it to tailor the answer towards what is most useful for that goal.
The response will contain a direct answer to the question and relevant excerpts and sources from the documentation.
Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.