Clara Parabricks v4.2.0
NVIDIA Parabricks v4.2.0


Annotate variants based on a PON file and modify the "INFO" field of the input VCF file. This is the post process of calling --pon in mutect.


# 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 \ \ pbrun postpon \ --in-vcf /workdir/${INPUT_VCF} \ --in-pon-file /workdir/${INPUT_PON_VCF} \ --out-vcf /outputdir/${OUTPUT_VCF}

Annotate variants based on a PON file

Input/Output file options

--in-vcf IN_VCF

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

Option is required.

--in-pon-file IN_PON_FILE

Path to the input PON 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


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)


Do not delete the directory storing temporary files after completion.


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


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