our Python client for services python sync_sulab

We are happy to announce that the official Python client ("") for our web services is now available from PyPI (the Python Package Index). allows users to annotate or query for human variants, either a single variant or a list of variants, without making explicit GET or POST web service calls. This is especially convenient for users who are already handling a large number of variants using Python scripts.

Backed by the high-performance web services, can access integrated annotations for over 280M variants, including annotations from ClinVar, COSMIC, CADD, ExAC , etc (see here for the complete list of data sources). We always keep the annotations up-to-date and keep expanding the data sources, so that users don't have to download and maintain their own local copy of annotation databases.

To give it a try, simply install it via pip:

pip install myvariant

The core functionality of package is encapsulated in its MyVariantInfo class:

In [1]: import myvariant
In [2]: mv = myvariant.MyVariantInfo()

which provides four methods:

  • getvariants
    to retrieve the annotations for a list of variants by their HGVS ids:
mv.getvariants(['chr1:g.866422C>T', 'chr1:g.876664G>A','chr1:g.69635G>C'])
mv.query("cosmic.tumor_site:liver", fields='cosmic')
  • querymany
    to query matching variants for a list of alternative ids or query terms:
mv.querymany(['RCV000083620', 'RCV000083584'],
scopes='clinvar.rcv_accession', fields='clinvar')

To help generate the valid HGVS-ids from popular VCF-style chrom, pos, alt, ref values, a helper function myvariant.format_hgvs is also provided:

In [3]: myvariant.format_hgvs("1", 35366, "C", "T")
Out[3]: 'chr1:g.35366C>T'

In [4]: myvariant.format_hgvs('2', 17142, "G", "GA")
Out[4]: 'chr2:g.17142_17143insA'

In [5]: myvariant.format_hgvs("MT", 8270, "CACCCCCTCT", "C")
Out[5]: 'chrMT:g.8271_8279del'

In [6]: myvariant.format_hgvs("X", 107930849, "GGA", "C")
Out[6]: 'chrX:g.107930849_107930851delinsC'

You can find more usage examples from PyPI page. The detailed API documentation can be found at . If you dive even deeper, you may find our extensive test code here can also serve as pretty good usage examples.

Feedbacks? We are always available at or @myvariantinfo.