Getting Started

1. Signup

import Agvd from "agvd";

const handle = new Agvd();
handle.signup({
  id: 'user-id',
  name: 'Full Name',
  email: '[email protected]',
  password: 'John2022@Doe',
  organization: 'H3ABioNet'
});

2. Login

import Agvd from "agvd";

const handle = new Agvd();
handle.login({
  user: 'user_id',
  password: 'user_password'
});

3 Variant Query

You need to be authenticated to for you to query the AGVD. On login, a token shall be supplied with which you'll submit as an argument to the query function.

import Agvd from "agvd";

const handle = new Agvd();
handle.query({
  token: 'insert-token-here',
  id: '10:188836:A:G'
});

Alternatively you can to avoid the initial login step, you can submit your both your userid and password as parameters as arguments to the query function

import Agvd from "agvd";

const handle = new Agvd();
handle.query({
  user: 'insert-user-id-here',
  password: 'insert-your-password-here',
  id: '10:188836:A:G'
});

Allowed Query Parameters

Allowed Keyword Arguments	Description	Example
token	A token supplied after user login; If user doesn't want to log in first before making the query, the user can append their user-id and password as keyword parameters in the query function
user	unique user-id
password	user password
id	List of IDs, these can be rs IDs (dbSNP) or variants in the format chrom:start:ref:alt	rs116600158, COSM6350960, 19:7177679:C:T
region	List of regions, these can be just a single chromosome name or regions in the format :-	chr22, 3:100000-200000
type	List of types, accepted values are SNV, MNV, INDEL, SV, CNV, INSERTION, DELETION	SNV, INDEL
gene	List of genes, most gene IDs are accepted (HGNC, Ensembl gene, ...).	BRCA2, BMPR, ENSG00000174173, ENST00000495642
sample	Filter variants where the samples contain the variant (HET or HOM_ALT). Accepts AND ( ; ) and OR ( , ) operators.	HG0097,HG00978
cohort	Select variants with calculated stats for the selected cohorts
cohortStatsRef	Reference Allele Frequency	ALL>0.6
cohortStatsAlt	Alternate Allele Frequency	ALL<=4
cohortStatsMaf	Minor Allele Frequency	ALL<0.01
cohortStatsMgf	Minor Genotype Frequency	COH1<0.1,COH2<0.3
clinicalSignificance	Clinical significance: benign, likely_benign, likely_pathogenic, pathogenic