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Showing content from http://www.ensembl.org/info/docs/tools/vep/recoder/index.html below:

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.Met259Thr) 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.

Web interface

The Variant Recoder web interface allows you to simply enter variant names and identifiers in a variety of formats and obtain VCF and other names/descriptions.

Input form

First select the correct species for your data.
You can optionally choose a name for the data you upload - this can make it easier for you to identify jobs and files that you have uploaded to the Variant Recoder at a later point.
You have two options for uploading your data:
- File upload - click the "Choose file" button and locate the file on your system
- Paste file - simply copy and paste the contents of your file into the large text box
Once you have uploaded some data, you can select it as the input for future jobs by choosing the data from the drop down menu. We recommend uploading small sets of data.
The format of your data is automatically detected; the supported input data is:
We also support ambiguous descriptions listing only gene symbol and protein change (e.g. BRCA2:p.Trp31Cys), as seen in the literature.
Results: you can choose which type of data format to return. The supported formats are the same as the input plus the format VCF.

Output

There is an output line for each alternative allele of the input variant. Each output value is annexed to the corresponding alternative allele with the exception of COSMIC and HGMD IDs.

In the output table you can click on links that will take you to known variants, where available, genomic locations or gene and transcript information.

Example of output, variant with two alternative alleles:

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

Command line tool

Download and install

Variant Recoder is part of the VEP package.

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

Note

Because Variant Recoder depends on database access for identifier lookup, and cannot be used in offline mode as per VEP, you don't need to download the VEP cache files (which will be asked during the installation process).

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

Output is a JSON array of objects, one per input variant, with the following keys:

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)
var_synonyms: Extra known synonyms for co-located variants (optional)
mane_select: MANE Select (Matched Annotation from NCBI and EMBL-EBI) Transcripts. (optional) Note: only available for human.
warnings: Warnings generated e.g. for invalid HGVS

Tips

Use --pretty to pre-format and indent JSON output.

Example of output, with the --pretty flag:

./variant_recoder --id "AGT:p.Met259Thr" --pretty

[
   {
     "warnings" : [
         "Possible invalid use of gene or protein identifier 'AGT' as HGVS reference; AGT:p.Met259Thr may resolve to multiple genomic locations"
      ],
      "C" : {
        "input" : "AGT:p.Met259Thr",
        "id" : [
           "rs699",
           "CM920010",
           "COSV64184214"
        ],
        "hgvsg" : [
           "NC_000001.11:g.230710048A>G"
        ],
        "hgvsc" : [
           "ENST00000366667.6:c.776T>C",
           "ENST00000679684.1:c.776T>C",
           "ENST00000679738.1:c.776T>C",
           "ENST00000679802.1:c.776T>C",
           "ENST00000679854.1:n.1287T>C",
           "ENST00000679957.1:c.776T>C",
           "ENST00000680041.1:c.776T>C",
           "ENST00000680783.1:c.776T>C",
           "ENST00000681269.1:c.776T>C",
           "ENST00000681347.1:n.1287T>C",
           "ENST00000681514.1:c.776T>C",
           "ENST00000681772.1:c.776T>C",
           "NM_001382817.3:c.776T>C",
           "NM_001384479.1:c.776T>C"
        ],
        "hgvsp" : [
           "ENSP00000355627.5:p.Met259Thr",
           "ENSP00000505981.1:p.Met259Thr",
           "ENSP00000505063.1:p.Met259Thr",
           "ENSP00000505184.1:p.Met259Thr",
           "ENSP00000506646.1:p.Met259Thr",
           "ENSP00000504866.1:p.Met259Thr",
           "ENSP00000506329.1:p.Met259Thr",
           "ENSP00000505985.1:p.Met259Thr",
           "ENSP00000505963.1:p.Met259Thr",
           "ENSP00000505829.1:p.Met259Thr",
           "NP_001369746.2:p.Met259Thr",
           "NP_001371408.1:p.Met259Thr"
        ],
        "spdi" : [
           "NC_000001.11:230710047:A:G"
        ],
     }
   }
]

Options

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

However some other flags are unique to variant_recoder:

Flag Alternate Description

--input_data [input_string]

-id

A single variant as a string, such as:

variant identifiers

e.g.:

--id rs699

HGVS notations

e.g.:

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

SPDI notation

e.g.:

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

e.g.:

--id "1  230710048  rs699  A  G"

VEP default input format

e.g.:

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

--input_file [input_file]

-i

Input file containing one or more variants, one per line. Mixed formats is disallowed.
Here are the input formats supported:

--species

Species to use. Default value: homo_sapiens

--grch37

Use GRCh37 assembly instead of GRCh38

--genomes

Set database parameters for Ensembl Genomes species

--pretty

Write pre-formatted indented JSON

--vcf_string

Returns the VCF format in a string

--var_synonyms

Extra known synonyms for co-located variants

--mane_select

Returns MANE Select transcripts in HGVS format (e.g. hgvsg, hgvsc, hgvsp). Only available for human.

--fields [field1,field2]

Limit the default output fields. Comma-separated list, one or more of: id, hgvsg, hgvsc, hgvsp, spdi. e.g.:

./variant_recoder --id "AGT:p.Met259Thr" --fields id,hgvsc

--host [db_host]

Change database host from default ensembldb.ensembl.org (UK).
Geographic mirrors are useastdb.ensembl.org (US East Coast) and asiadb.ensembl.org (Asia).
Other flags such as --user, --port and --pass may also be set.

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

Set and customise transcript selection process, see VEP documentation

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