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 section for a detailed listing of all available options.

Quick Start

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# This command assumes all the inputs are in the current working directory and all the outputs go to the same place.
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docker run --rm --gpus all --volume $(pwd):/workdir --volume $(pwd):/outputdir \
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    --workdir /workdir \
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    nvcr.io/nvidia/clara/clara-parabricks:4.7.1-1 \
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    pbrun dbsnp \
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    --in-vcf /workdir/${INPUT_VCF} \
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    --out-vcf /outputdir/${OUTPUT_VCF} \
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    --in-dbsnp-file /workdir/${DBSNP_DATABASE}

Options