postpon

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.

See the postpon Reference section for a detailed listing of all available options.

Quick Start

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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:4.3.2-1 (OR nvcr.io/nvidia/clara/clara-parabricks:4.3.2-1.grace) \
    pbrun postpon \
    --in-vcf /workdir/${INPUT_VCF} \
    --in-pon-file /workdir/${INPUT_PON_VCF} \
    --out-vcf /outputdir/${OUTPUT_VCF}

postpon Reference

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.

GPU options:

--num-gpus NUM_GPUS: Number of GPUs to use for a run. GPUs 0..(NUM_GPUS-1) will be used.

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