Variant Recoder

Variant Recoder is a tool for translating between different variant names. It accepts HGVS descriptions and variant identifiers from databases such as dbSNP, ClinVar, UniProt and PharmGKB (see full list of accession databases) as input.

Some forms of ambiguous and incorrect HGVS descriptions are supported including those stating only gene name and protein change (eg. AGT:p.Met268Thr) which are often seen in publications.

For each input variant, variant_recoder reports the variant identifiers held in Ensembl and HGVS genomic, transcript and protein descriptions on Ensembl, RefSeq and LRG sequences.

REST API

Ensembl provides a REST API for Variant Recoder with 2 endpoints:

• Single variant query: GET variant_recoder
• Multiple variants query: POST variant_recoder

Download and install

Variant Recoder is part of the VEP package.

Please follow the instructions about the download and installation of VEP.

Usage

Variant Recoder depends on database access for identifier lookup, and cannot be used in offline mode as per VEP.

The output format is JSON and the JSON Perl module is required.

# Running on one ID, as a string:
./variant_recoder --id [input_data_string]

# Running on several IDs, in a text file:
./variant_recoder -i [input_file] --species [species]

Like VEP, Variant Recoder can use VCF, variant identifiers, HGVS notations and SPDI in addition to the VEP default format as input.

Output

• input: input string
• id: variant identifiers
• hgvsg: HGVS genomic nomenclature
• hgvsc: HGVS transcript nomenclature
• hgvsp: HGVS protein nomenclature
• spdi: Genomic SPDI notation
• vcf_string: VCF format (optional)
• warnings: Warnings generated e.g. for invalid HGVS

Example of output, with the --pretty flag:

./variant_recoder --id "AGT:p.Met268Thr" --pretty

[
   {
      "input" : "AGT:p.Met268Thr",
      "id" : [
         "rs699",
         "CM920010"
      ],
      "hgvsg" : [
         "NC_000001.11:g.230710048A>G"
      ],
      "hgvsc" : [
         "ENST00000366667.4:c.803T>C",
         "NM_000029.3:c.803T>C"
      ],
      "hgvsp" : [
         "ENSP00000355627.4:p.Met268Thr",
         "NP_000020.1:p.Met268Thr"
      ],
      "spdi" : [
         "NC_000001.11:230710047:A:G"
      ],
      "warnings" : [
         "Possible invalid use of gene name 'AGT' as HGVS reference; AGT:p.Met268Thr may resolve to multiple genomic locations"
      ]
   }
]

Options

Variant Recoder shares many of the same command line flags as VEP.

However some other flags are unique to variant_recoder:

--input_data [input_string]

-id

--id rs699

--id "ENST00000366667.4:c.803T>C"

--id "NC_000001.11:230710047:A:G"

--id "1  230710048  rs699  A  G"

--id "1  230710048   230710048  A/G  +"

--input_file [input_file]

-i

--species

--grch37

--genomes

--pretty

--fields [field1,field2]

./variant_recoder --id "AGT:p.Met268Thr" --fields id,hgvsc

--host [db_host]

--pick, --per_gene, --pick_allele,
--pick_allele_gene, --pick_order