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varity

Clojars Project build codecov

Variant translation library for Clojure.

Features

  • VCF variant ⇄ HGVS
  • Finding HGVS aliases
  • Conversion of a genomic coordinates between assemblies

Installation

Clojure CLI/deps.edn:

varity/varity {:mvn/version "0.11.0"}

Leiningen/Boot:

[varity "0.11.0"]

To use varity with Clojure 1.8, you must include a dependency on clojure-future-spec.

Breaking changes in 0.11.0

We fixed the varity.vcf-to-hgvs implementation. It is confusing to throw the exception in vcf-variant->protein-hgvs when a variant overlaps the exon-intron boundaries, even if coding DNA HGVS is available. So we changed the behavior to return protein HGVS as nil.

Usage

Documentation

API Reference

Notice

All positions are represented as one-based number, and all ranges are represented as one-based closed intervals. For example,

{:pos 3}

represents the third position from the start, and

{:chr "chr1", :start 1, :end 3}

represents the first three bases of chromosome 1.

VCF variant to HGVS

varity.vcf-to-hgvs provides functions to convert a VCF-style variant into HGVS. The returned HGVS is data structure of clj-hgvs.

(require '[varity.vcf-to-hgvs :as v2h])

(v2h/vcf-variant->hgvs {:chr "chr7", :pos 55191822, :ref "T", :alt "G"}
                       "path/to/hg38.fa" "path/to/refGene.txt.gz")
;;=> ({:coding-dna #clj-hgvs/hgvs "NM_005228:c.2573T>G",
;;     :protein #clj-hgvs/hgvs "p.L858R"})

Use clj-hgvs.core/format to obtain HGVS text.

(require '[clj-hgvs.core :as hgvs])

(def l858r (-> (v2h/vcf-variant->protein-hgvs {:chr "chr7", :pos 55191822, :ref "T", :alt "G"}
                                              "path/to/hg38.fa" "path/to/refGene.txt.gz")
               first))

(hgvs/format l858r {:amino-acid-format :long})
;;=> "p.Leu858Arg"

HGVS to VCF variants

varity.hgvs-to-vcf provides functions to convert HGVS into VCF-style variants.

(require '[varity.hgvs-to-vcf :as h2v]
         '[clj-hgvs.core :as hgvs])

(h2v/hgvs->vcf-variants #clj-hgvs/hgvs "NM_005228:c.2573T>G" "path/to/hg38.fa" "path/to/refGene.txt.gz")
;;=> ({:chr "chr7", :pos 55191822, :ref "T", :alt "G"})

(h2v/hgvs->vcf-variants #clj-hgvs/hgvs "c.2573T>G" "EGFR" "path/to/hg38.fa" "path/to/refGene.txt.gz")
;;=> ({:chr "chr7", :pos 55191822, :ref "T", :alt "G"})

(h2v/hgvs->vcf-variants #clj-hgvs/hgvs "p.A222V" "MTHFR" "path/to/hg38.fa" "path/to/refGene.txt.gz")
;;=> ({:chr "chr1", :pos 11796320, :ref "GG", :alt "CA"}
;;    {:chr "chr1", :pos 11796320, :ref "GG", :alt "AA"}
;;    {:chr "chr1", :pos 11796320, :ref "GG", :alt "TA"}
;;    {:chr "chr1", :pos 11796321, :ref "G", :alt "A"})

Finding HGVS aliases

varity.hgvs/find-aliases finds alternative HGVS expressions for the same variant.

(require '[varity.hgvs :as vhgvs])

(vhgvs/find-aliases #clj-hgvs/hgvs "NM_000059:c.162CAA[1]"
                    "path/to/hg38.fa" "path/to/refGene.txt.gz")
;;=> (#clj-hgvs/hgvs "NM_000059:c.162CAA[1]"
;;    #clj-hgvs/hgvs "NM_000059:c.165_167delCAA")

Conversion of a genomic coordinate between assemblies

To convert a genomic coordinate between assemblies,

(require '[varity.lift :as lift])

(lift/convert-coord {:chr "chr1", :pos 743267} "path/to/hg19ToHg38.over.chain.gz")
;;=> {:chr "chr1", :pos 807887}

License

Copyright 2017-2022 Xcoo, Inc.

Licensed under the Apache License, Version 2.0.

Acknowledgements

The algorithm of varity.fusion was initially developed by Norio Tanaka at Cancer Precision Medicine Center, Japanese Foundation for Cancer Research. We thank him for his scientific insight and technical help.