dbsnp - NVIDIA Docs

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.

See the dbsnp Reference section for a detailed listing of all available options.

Quick Start

Copy
Copied!

            
            # 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 $(pwd):/outputdir \
    --workdir /workdir \
    nvcr.io/nvidia/clara/clara-parabricks:4.5.1-1 \
    pbrun dbsnp \
    --in-vcf /workdir/${INPUT_VCF} \
    --out-vcf /outputdir/${OUTPUT_VCF} \
    --in-dbsnp-file /workdir/${DBSNP_DATABASE}

dbsnp Reference

Annotate variants based on a dbSNP.

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	‑‑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.