postpon

NVIDIA Clara Parabricks v4.0.0

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.

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# This command assumes all the inputs are in and all the outputs go to . $ docker run --rm --gpus all --volume <INPUT_DIR>:/workdir --volume <OUTPUT_DIR>:/outputdir -w /workdir \ nvcr.io/nvidia/clara/clara-parabricks:4.0.0-1 \ 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

(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 2022, Nvidia. Last updated on Jun 28, 2023.