Nvidia Clara Parabricks dbsnp

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}