| Package | dna2json |
| Description | Formats your DNA file as JSON |
| Node Version | >= 0.4 |
A SNP (single-nucleotide polymorphism - pronounced "snip") is a mutation in your genome. SNPs can tell you a lot about yourself (hair color, height, muscle type, allergies, response to disease, response to pharmaceuticals, heritage, etc.).
Your DNA file from any vendor will be a big list of these SNPs. Think of it like a diff against a reference human genome. Most vendors will compare your genome against GRCh Build 37
| Name | Supported | Price | Sample | Autosomal SNPs | Y SNPs | X SNPs | MT SNPs | Raw Data |
|---|---|---|---|---|---|---|---|---|
| 23andMe | Yes | 99 USD | Saliva | 967,000 | 3,089 | 26,087 | 2,737 | Yes |
| ancestryDNA | Yes | 99 USD | Saliva | 682,549 | 885 | 17,604 | 0 | Yes |
| FamilyTree | Yes | 99 USD | Cheek Swab | 708,092 | 0 | 18,091 | 0 | Yes |
tl;dr use 23andMe they provide more data and are the cheapest
Use this if you just want to convert your data to the correct format so you can start querying your genome.
$ npm install dna2json -g
$ dna2json
Usage: dna2json <input file> <output file>
$ dna2json dna.txt dna.json
This will take a while...
It will stream the SNPs to disk as JSON - pretty easy.
var dna = require('dna2json');
var JSONStream = require('JSONStream');
var fs = require('fs');
// dna.createParser() returns a duplex stream
// input = text from your dna file
// output = SNPs as JSON
// to write to disk just pipe it to JSONStream then to fs
fs.createReadStream("dna.txt")
.pipe(dna.createParser())
.pipe(JSONStream.stringify())
.pipe(fs.createWriteStream("dna.json"));Every vendor has their own format for your DNA. I decided to make a standard format called SNP-JSON. This library will convert custom formats to this standard.
SNP-JSON looks like this
[
{"id":"rs10749813","c":1,"pos":73557945,"g":null},
{"id":"rs4128552","c":1,"pos":73560811,"g":"GT"},
{"id":"rs12033354","c":1,"pos":73573941,"g":"AG"},
{"id":"rs4603080","c":1,"pos":73579237,"g":"AG"},
{"id":"rs4582739","c":1,"pos":73602381,"g":"CT"},
{"id":"rs4452995","c":1,"pos":73613560,"g":"CT"}
]Explanation:
| Key | Description |
|---|---|
| id | RSID or vendor ID |
| c | Chromosome (1-22, X, Y, or MT) |
| pos | GRCh position |
| g | Genotype |
Once you have your data in the right format you can use the library of genosets by genomejs.
You can view a list of these at this npm search
You can also make your own tools that analyze your DNA however you want. It's yours! Here is a tool that will help query your DNA GQL
(MIT License)
Copyright (c) 2013 Fractal contact@wearefractal.com
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