Variant Effect Predictor Running VEP

--help

--quiet

-q

--verbose

-v

--config [filename]

Load configuration options from a config file. The config file should consist of whitespace-separated pairs of option names and settings e.g.:

output_file   my_output.txt
species       mus_musculus
format        vcf
host          useastdb.ensembl.org

--everything

-e

--sift b, --polyphen b, --ccds, --hgvs, --symbol, --numbers, --domains, --regulatory, --canonical, --protein, --biotype, --uniprot, --tsl, --appris, --gene_phenotype --af, --af_1kg, --af_esp, --af_gnomad, --max_af, --pubmed, --var_synonyms, --variant_class, --mane

--species [species]

--assembly [name]

-a

--input_file [filename]

-i

--input_data [string]

--id

Raw input data as a string. May be used, for example, to input a single rsID or HGVS notation quickly to vep:

--input_data rs699

--format [format]

Input file format - one of "ensembl", "vcf", "hgvs", "id", "region", "spdi".
By default, VEP auto-detects the input file format. Using this option you can specify the input file is Ensembl, VCF, IDs, HGVS, SPDI or region format. Can use compressed version (gzipped) of any file format listed above. Auto-detects format by default

--output_file [filename]

-o

--force_overwrite

--force

--stats_file [filename]

--sf

--no_stats

--stats_text

--warning_file [filename]

--max_sv_size

--no_check_variants_order

--fork [num_forks]

--cache

--dir [directory]

--dir_cache [directory]

--dir_plugins [directory]

--offline

--fasta [file|dir]

--fa

--refseq

Specify this option if you have installed the RefSeq cache in order for VEP to pick up the alternate cache directory. This cache contains transcript objects corresponding to RefSeq transcripts. Consequence output will be given relative to these transcripts in place of the default Ensembl transcripts (see documentation)

--merged

Use the merged Ensembl and RefSeq cache. Consequences are flagged with the SOURCE of each transcript used.

--cache_version

--show_cache_info

--buffer_size [number]

--plugin [plugin name]

--custom [filename]

--gff [filename]

--gtf [filename]

--bam [filename]

--use_transcript_ref

--use_given_ref

--custom_multi_allelic

--vcf

Writes output in VCF format. Consequences are added in the INFO field of the VCF file, using the key "CSQ". Data fields are encoded separated by "|"; the order of fields is written in the VCF header. Output fields in the "CSQ" INFO field can be selected by using --fields.

If the input format was VCF, the file will remain unchanged save for the addition of the CSQ field (unless using any filtering).

Custom data added with --custom are added as separate fields, using the key specified for each data file.

Commas in fields are replaced with ampersands (&) to preserve VCF format.

--tab

--json

--compress_output [gzip|bgzip]

--fields [list]

Configure the output format using a comma separated list of fields.
Can only be used with tab (--tab) or VCF format (--vcf) output.
For the tab format output, the selected fields may be those present in the default output columns, or any of those that appear in the Extra column (including those added by plugins or custom annotations) if the appropriate output is available (e.g. use --show_ref_allele to access 'REF_ALLELE'). Output remains tab-delimited.
For the VCF format output, the selected fields are those present within the "CSQ" INFO field.

Example of command for the tab output:

--tab --fields "Uploaded_variation,Location,Allele,Gene"

Example of command for the VCF format output:

--vcf --fields "Allele,Consequence,Feature_type,Feature"

--minimal

--variant_class

--sift [p|s|b]

--polyphen [p|s|b]

--humdiv

--nearest [transcript|gene|symbol]

Retrieve the transcript or gene with the nearest protein-coding transcription start site (TSS) to each input variant. Use "transcript" to retrieve the transcript stable ID, "gene" to retrieve the gene stable ID, or "symbol" to retrieve the gene symbol. Note that the nearest TSS may not belong to a transcript that overlaps the input variant, and more than one may be reported in the case where two are equidistant from the input coordinates.

Currently only available when using a cache annotation source, and requires the Set::IntervalTree perl module.

--distance [bp_distance(,downstream_distance_if_different)]

--overlaps

--gene_phenotype

--regulatory

--cell_type

--individual [all|ind list]

--phased

--allele_number

--show_ref_allele

--total_length

--numbers

--no_escape

--keep_csq

--vcf_info_field [CSQ|ANN|(other)]

--terms [SO|display|NCBI]

-t

--no_headers

--shift_3prime [0|1]

--shift_genomic [0|1]

--shift_length

--hgvs

--hgvsg

--spdi

--shift_hgvs [0|1]

--transcript_version

--protein

--symbol

--ccds

--uniprot

--tsl

--appris

--canonical

--mane

--mane_select

--biotype

--domains

--xref_refseq

--synonyms [file]

--check_existing

--check_svs

--clin_sig_allele [1|0]

--exclude_null_alleles

--no_check_alleles

--af

--max_af

--af_1kg

--af_esp

--af_gnomad

--af_exac

--pubmed

--var_synonyms

--failed [0|1]

--gencode_basic

--exclude_predicted

--transcript_filter

ADVANCED Filter transcripts according to any arbitrary set of rules. Uses similar notation to filter_vep.

You may filter on any key defined in the root of the transcript object; most commonly this will be "stable_id":

--transcript_filter "stable_id match N[MR]_"

--check_ref

--lookup_ref

--dont_skip

--allow_non_variant

--chr [list]

--coding_only

--no_intergenic

--pick

--pick_allele

--per_gene

--pick_allele_gene

--flag_pick

--flag_pick_allele

--flag_pick_allele_gene

--pick_order [c1,c2,...,cN]

Customise the order of criteria (and the list of criteria) applied when choosing a block of annotation data with one of the following options: --pick, --pick_allele, --per_gene, --pick_allele_gene, --flag_pick, --flag_pick_allele, --flag_pick_allele_gene. See this page for the default order.
Valid criteria are: [ canonical appris tsl biotype ccds rank length mane ]. e.g.:

--pick --pick_order tsl,appris,rank

--most_severe

--summary

--filter_common

--check_frequency

--freq_pop [pop]

--freq_freq [freq]

--freq_gt_lt [gt|lt]

--freq_filter [exclude|include]

--database

--host [hostname]

--user [username]

-u

--password [password]

--pass

--port [number]

--genomes

--is_multispecies [0|1]

--lrg

--db_version [number]

--registry [filename]