varity

Variant translation library for Clojure.

Features

• VCF variant ⇄ HGVS
• Conversion between assemblies

Installation

With Leiningen/Boot:

[varity "0.4.1"]

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")
;;=> ({:cdna {:kind :cdna,
;;            :mutation #clj_hgvs.mutation.DNASubstitution
;;            {:alt "G",
;;             :coord #clj_hgvs.coordinate.CDNACoordinate
;;             {:offset 0, :position 2573, :region nil},
;;             :ref "T",
;;             :type ">"},
;;            :transcript "NM_005228"},
;;     :protein {:kind :protein,
;;               :mutation #clj_hgvs.mutation.ProteinSubstitution
;;               {:alt "Arg",
;;                :coord #clj_hgvs.coordinate.ProteinCoordinate
;;                {:position 858},
;;                :ref "Leu"},
;;               :transcript nil}})

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 :short})
;;=> p.L858R

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 (hgvs/parse "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 (hgvs/parse "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 (hgvs/parse "p.A222V") "MTHFR" "path/to/hg38.fa" "path/to/refGene.txt.gz")
;;=> ({:chr "chr1", :pos 11796321, :ref "G", :alt "A"})

Conversion between assemblies

To convert a genome 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 2017-2018 Xcoo, Inc.

Licensed under the Apache License, Version 2.0.