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.

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# 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 \ --workdir /workdir \ nvcr.io/nvidia/clara/clara-parabricks:4.2.1-1 \ pbrun dbsnp \ --in-vcf /workdir/${INPUT_VCF} \ --out-vcf /outputdir/${OUTPUT_VCF} \ --in-dbsnp-file /workdir/${DBSNP_DATABASE}

Annotate variants based on a dbSNP.

Input/Output file options

--in-vcf IN_VCF

Path to the input VCF file. (default: None)

Option is required.

--in-dbsnp-file IN_DBSNP_FILE

Path to the input DBSNP file in vcf.gz format, with its tabix index. (default: None)

Option is required.

--out-vcf OUT_VCF

Output annotated VCF file. (default: None)

Option is required.

Options specific to this tool

(none)

Common options:

--logfile LOGFILE

Path to the log file. If not specified, messages will only be written to the standard error output. (default: None)

--tmp-dir TMP_DIR

Full path to the directory where temporary files will be stored.

--with-petagene-dir WITH_PETAGENE_DIR

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 (default: None)

--keep-tmp

Do not delete the directory storing temporary files after completion.

--no-seccomp-override

Do not override seccomp options for docker (default: None).

--version

View compatible software versions.

© Copyright 2024, Nvidia. Last updated on Jan 9, 2024.