bactopia-mask-consensus
Snippy consensus (subs) with coverage masking.
Usage
bactopia-mask-consensus SAMPLE REFERENCE FASTA VCF COVERAGE [OPTIONS]
Arguments
| Argument | Type | Required | Description |
|---|---|---|---|
SAMPLE | STRING | Yes | Name of the input sample. |
REFERENCE | STRING | Yes | The reference assembly accession. |
FASTA | STRING | Yes | The consensus FASTA file. |
VCF | STRING | Yes | The VCF file with called substitutions. |
COVERAGE | STRING | Yes | The per-base coverage file. |
Options
| Option | Type | Default | Description |
|---|---|---|---|
--version, -V | BOOL | false | Show the version and exit. |
--mincov | INT | 10 | Minimum required coverage to not mask. |