```bash
docker run --rm quay.io/biocontainers/ensembl-vep:115.2--pl5321h2a3209d_1 filter_vep --help
```

#------------#
# filter_vep #
#------------#

http://www.ensembl.org/info/docs/tools/vep/script/vep_filter.html

Usage:
./filter_vep [arguments]
  
--help               -h   Print usage message and exit

--input_file [file]  -i   Specify the input file (i.e. the VEP results file).
                          If no input file is specified, the script will
                          attempt to read from STDIN. Input may be gzipped - to
                          force the script to read a file as gzipped, use --gz
--format [vcf|tab]        Specify input file format (tab for any tab-delimited
                          format, including default VEP output format)

--output_file [file] -o   Specify the output file to write to. If no output file
                          is specified, the script will write to STDOUT
--force_overwrite         Force the script to overwrite the output file if it
                          already exists

--filter [filters]   -f   Add filter. Multiple --filter flags may be used, and
                          are treated as logical ANDs, i.e. all filters must
                          pass for a line to be printed

--list               -l   List allowed fields from the input file
--count              -c   Print only a count of matched lines

--only_matched            In VCF files, the CSQ field that contains the
                          consequence data will often contain more than one
                          "block" of consequence data, where each block
                          corresponds to a variant/feature overlap. Using
                          --only_matched will remove blocks that do not pass the
                          filters. By default, the script prints out the entire
                          VCF line if any of the blocks pass the filters.

--vcf_info_field [key]    With VCF input files, by default filter_vep expects to
                          find VEP annotations encoded in the CSQ INFO key; VEP
                          itself can be configured to write to a different key
                          (with the equivalent --vcf_info_field flag). Use this
                          flag to change the INFO key VEP expects to decode.
                          
--ontology           -y   Use Sequence Ontology to match consequence terms. Use
                          with operator "is" to match against all child terms of
                          your value.
                          e.g. "Consequence is coding_sequence_variant" will
                          match missense_variant, synonymous_variant etc.
                          Requires database connection; defaults to connecting
                          to ensembldb.ensembl.org. Use --host, --port, --user,
                          --password, --version as per ./vep to change
                          connection parameters.
