VARCODE(1)

NAME
varcode - Annotates variants with overlapping gene names and predicted coding effects

DESCRIPTION
Varcode

    Version: 1.2.1 Path: /usr/lib/python3/dist-packages/varcode

usage: varcode [-h] [--vcf VCF] [--maf MAF] [--variant CHR POS REF ALT]

    [--genome GENOME] [--download-reference-genome-data] [--json-variants JSON_VARIANTS] [--output-csv OUTPUT_CSV] [--one-per-variant] [--only-coding]

  options:

-h, --help
    show this help message and exit

--output-csv OUTPUT_CSV
    Output path to CSV

--one-per-variant
    Only return highest priority effect overlapping a variant, otherwise all overlapping transcripts are returned.

--only-coding
    Filter silent and non-coding effects

  Variants:

    Genomic variant files

--vcf VCF
    Genomic variants in VCF format

--maf MAF
    Genomic variants in TCGA's MAF format

--variant CHR POS REF ALT
    Individual variant as 4 arguments giving chromsome, position, ref, and alt. Example: chr1 3848 C G. Use '.' to indicate empty alleles for insertions or deletions.

--genome GENOME
    What reference assembly your variant coordinates are using. Examples: 'hg19', 'GRCh38', or 'mm9'. This argument is ignored for MAF files, since each row includes the reference. For VCF files, this is used if specified, and otherwise is guessed from the header. For variants specfied on the commandline with --variant, this option is required.

--download-reference-genome-data
    Automatically download genome reference data required for annotation using PyEnsembl. Otherwise you must first run 'pyensembl install' for the release/species corresponding to the genome used in your VCF.

--json-variants JSON_VARIANTS
    Path to Varcode.VariantCollection object serialized as a JSON file.

    Version: 1.2.1 Path: /usr/lib/python3/dist-packages/varcode

SEE ALSO
The full documentation for varcode is maintained as a Texinfo manual. If the info and varcode programs are properly installed at your site, the command

    info varcode

should give you access to the complete manual.