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Nvidia Clara Parabricks dbsnp

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Description

Annotate variants based on a variant database.

Publisher

Nvidia

Latest Tag

4.0.0-1

Modified

November 1, 2022

Compressed Size

89.13 MB

Multinode Support

No

Multi-Arch Support

No

4.0.0-1 (Latest) Scan Results

Linux / amd64

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.

For further information visit the dbsnp help page.

Quick Start

# This command assumes all the inputs are in <INPUT_DIR> and all the outputs go to <OUTPUT_DIR>.
$ docker run --rm --gpus all --volume <INPUT_DIR>:/workdir --volume <OUTPUT_DIR>:/outputdir
    -w /workdir \
    nvcr.io/nvidia/clara/clara-parabricks:<VERSION-TAG> \
    pbrun dbsnp \
    --in-vcf /workdir/${INPUT_VCF} \
    --out-vcf /outputdir/${OUTPUT_VCF} \
    --in-dbsnp-file /workdir/${DBSNP_DATABASE}