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# dbsnp

Annotate variants based on a variant database.

This tool annotates the variant calls within a VCF file using the dbSNP
database. The dbSNP database is a public archive of genetic variant
information, consisting of known variants and data on whether each of these are
considered to be neutral polymorphisms, polymorphisms with associated
phenotypes, or regions of no variation.

Refer to the [dbsnp Reference](#options) section for a detailed listing of all available options.

## Quick Start

```sh
# This command assumes all the inputs are in the current working directory and all the outputs go to the same place.
docker run --rm --gpus all --volume $(pwd):/workdir --volume $(pwd):/outputdir \
    --workdir /workdir \
    nvcr.io/nvidia/clara/clara-parabricks:4.8.0-1 \
    pbrun dbsnp \
    --in-vcf /workdir/${INPUT_VCF} \
    --out-vcf /outputdir/${OUTPUT_VCF} \
    --in-dbsnp-file /workdir/${DBSNP_DATABASE}
```

## Options

| Type    | Name                                    | Required? | Description                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 |
| ------- | --------------------------------------- | --------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| I/O     | `--in-vcf IN_VCF`                       | Yes       | Path to the input VCF file.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 |
| I/O     | `--in-dbsnp-file IN_DBSNP_FILE`         | Yes       | Path to the input DBSNP file in vcf.gz format, with its tabix index.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        |
| I/O     | `--out-vcf OUT_VCF`                     | Yes       | Output annotated VCF file.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  |
| Runtime | `--verbose`                             | No        | Enable verbose output.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |
| Runtime | `--x3`                                  | No        | Show full command line arguments.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           |
| Runtime | `--dry-run`                             | No        | Check if the current command is valid.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |
| Runtime | `--logfile LOGFILE`                     | No        | Path to the log file. If not specified, messages will only be written to the standard error output.                                                                                                                                                                                                                                                                                                                                                                                                                                                         |
| Runtime | `--tmp-dir TMP_DIR`                     | No        | Full path to the directory where temporary files will be stored. (default: .)                                                                                                                                                                                                                                                                                                                                                                                                                                                                               |
| Runtime | `--with-petagene-dir WITH_PETAGENE_DIR` | No        | Full path to the PetaGene installation directory. By default, this should have been installed at /opt/petagene. Use of this option also requires that the PetaLink library has been preloaded by setting the LD_PRELOAD environment variable. Optionally set the PETASUITE_REFPATH and PGCLOUD_CREDPATH environment variables that are used for data and credentials. Optionally set the PetaLinkMode environment variable that is used to further configure PetaLink, notably setting it to "+write" to enable outputting compressed BAM and .fastq files. |
| Runtime | `--keep-tmp`                            | No        | Do not delete the directory storing temporary files after completion.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       |
| Runtime | `--no-seccomp-override`                 | No        | Do not override seccomp options for docker.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 |
| Runtime | `--version`                             | No        | View compatible software versions.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          |
| Runtime | `--preserve-file-symlinks`              | No        | Override default behavior to keep file symlinks intact and *not* resolve the symlink.                                                                                                                                                                                                                                                                                                                                                                                                                                                                       |
| Runtime | `--help-json`                           | No        | Print out help message in JSON format.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |