Third-party packages

This page lists the third-party packages/modules built upon the services.

MyVariant python module

myvariant” is an easy-to-use Python wrapper to access services.

You can install it easily using either pip or easy_install:

pip install myvariant               #this is preferred


easy_install myvariant

This is a brief example:

In [1]: import myvariant

In [2]: mv = myvariant.MyVariantInfo()

In [3]: mv.getvariant('chr1:g.35367G>A')
{'_id': 'chr1:g.35367G>A',
 '_version': 1,
 'cadd': {'alt': 'A',
  'annotype': 'NonCodingTranscript',
  'bstatistic': 994,
  'chmm': {'bivflnk': 0.0,
   'enh': 0.0,
   'enhbiv': 0.0,
   'het': 0.0,
   'quies': 1.0,
   'reprpc': 0.0,
   'reprpcwk': 0.0,
   'tssa': 0.0,
   'tssaflnk': 0.0,
   'tssbiv': 0.0,
   'tx': 0.0,
   'txflnk': 0.0,
   'txwk': 0.0,
   'znfrpts': 0.0},
  'chrom': 1,
  'consdetail': 'non_coding_exon,nc',
  'consequence': 'NONCODING_CHANGE',
  'consscore': 5,
  'cpg': 0.03,
  'dna': {'helt': -2.04, 'mgw': 0.01, 'prot': 1.54, 'roll': -0.63},
  'encode': {'exp': 31.46, 'h3k27ac': 23.44, 'h3k4me1': 23.8, 'h3k4me3': 8.6},
  'exon': '2/3',
  'fitcons': 0.577621,
  'gc': 0.48,
  'gene': {'cds': {'cdna_pos': 476, 'rel_cdna_pos': 0.4},
   'feature_id': 'ENST00000417324',
   'gene_id': 'ENSG00000237613',
   'genename': 'FAM138A'},
  'gerp': {'n': 1.29, 's': -0.558},
  'isknownvariant': 'FALSE',
  'istv': 'FALSE',
  'length': 0,
  'mapability': {'20bp': 0, '35bp': 0},
  'min_dist_tse': 122,
  'min_dist_tss': 707,
  'mutindex': 70,
  'phast_cons': {'mammalian': 0.003, 'primate': 0.013, 'vertebrate': 0.003},
  'phred': 1.493,
  'phylop': {'mammalian': -0.155, 'primate': 0.151, 'vertebrate': -0.128},
  'pos': 35367,
  'rawscore': -0.160079,
  'ref': 'G',
  'scoresegdup': 0.99,
  'segway': 'D',
  'type': 'SNV'},
 'snpeff': {'ann': [{'effect': 'non_coding_exon_variant',
    'feature_id': 'NR_026818.1',
    'feature_type': 'transcript',
    'gene_id': 'FAM138A',
    'gene_name': 'FAM138A',
    'hgvs_c': 'n.476C>T',
    'putative_impact': 'MODIFIER',
    'rank': '2',
    'total': '3',
    'transcript_biotype': 'Noncoding'},
   {'effect': 'non_coding_exon_variant',
    'feature_id': 'NR_026820.1.2',
    'feature_type': 'transcript',
    'gene_id': 'FAM138F.2',
    'gene_name': 'FAM138F',
    'hgvs_c': 'n.476C>T',
    'putative_impact': 'MODIFIER',
    'rank': '2',
    'total': '3',
    'transcript_biotype': 'Noncoding'}]},
 'vcf': {'alt': 'A', 'position': '35367', 'ref': 'G'}}

See for more details.

MyVariant R package

An R wrapper for the API is available in Bioconductor since v3.2. To install:


To view documentation for your installation, enter R and type:


For more information, visit the Bioconductor myvariant page.

MyVariant Node.js package

myvariantjs is a Node.js wrapper for the API, developed and maintained by Larry Hengl. To install:

npm install myvariantjs --save

Some brief usage examples:

var mv = require('myvariantjs');
mv.getvariant('chr9:g.107620835G>A', ['dbnsfp.genename', 'cadd.phred']);

mv.getvariants("chr1:g.866422C>T,chr1:g.876664G>A,chr1:g.69635G>C");  // string of delimited ids
mv.getvariants(["chr1:g.866422C>T", "chr1:g.876664G>A","chr1:g.69635G>C"]);

mv.query("chr1:69000-70000", {fields:'dbnsfp.genename'});
mv.query("dbsnp.rsid:rs58991260", {fields:'dbnsfp'});

mv.querymany(['rs58991260', 'rs2500'], 'dbsnp.rsid');
mv.querymany(['RCV000083620', 'RCV000083611', 'RCV000083584'], 'clinvar.rcv_accession');

For more information, visit its API and usage docs, and its github code repository.

You can also check out this neat demo application developed by Larry using this myvariantjs package.

Another python module

This is another python wrapper of services created by Brian Schrader. The repository is available here.

You can install this package with PyPI like this:

pip install myvariant-api

A JBrowse plugin for and

JBrowse provides a fast, embeddable genome browser built completely with JavaScript and HTML5.

Colin from the JBrowse team made a very nice plugin to visualize the gene and variant annotations in JBrowse Genome Browser, using the data served from both and APIs.