Mutation annotations

SOPRANO has a specific format which is required to describe somatic mutations.

The format is most easily derived from a VCF file, or collection of VCF files. Users should use

soprano-annotate [-h] [--source SOURCE_PATH] [--output OUTPUT_NAME] [--cache CACHE_DIR] [--assembly ASSEMBLY]

-h | --help

Get help message.

-s | --source

Provide the path to a single VCF file, or a directory containing VCF files.

-o | --output

Provide a name for the output file. If not provided, when applied to as single input file, will default to the input file name with a .anno extension. If multiple files are selected (via prescribing a directory), this will field is required.

-d | --cache

Provide a path to a directory to cache the output inside of. Defaults to /app_sources/annotated_inputs.

-a | --assembly

Provide a genome assembly that is compatible with the input VCF source files. By default, this assumed to be GRCh38.

-k | --keep_missing

(N/Y) Choose to continue if there is a file that doesn't work in a large batch rather than failing all. Default is N, to fail.