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.
Refer to the postpon Reference section for a detailed listing of all available options.
Quick Start
1 # This command assumes all the inputs are in the current working directory and all the outputs go to the same place. 2 docker run --rm --gpus all --volume $(pwd):/workdir --volume $(pwd):/outputdir \ 3 --workdir /workdir \ 4 nvcr.io/nvidia/clara/clara-parabricks:4.7.1-1 \ 5 pbrun postpon \ 6 --in-vcf /workdir/${INPUT_VCF} \ 7 --in-pon-file /workdir/${INPUT_PON_VCF} \ 8 --out-vcf /outputdir/${OUTPUT_VCF}
Options
| Type | Name | Required? | Description |
|---|---|---|---|
| I/O | --in-vcf IN_VCF | Yes | Path to the input VCF file. |
| I/O | --in-pon-file IN_PON_FILE | Yes | Path to the input PON file in vcf.gz format with its tabix index. |
| I/O | --out-vcf OUT_VCF | Yes | Output annotated VCF file. |
| Runtime | --verbose | No | Enable verbose output. |
| Runtime | --x3 | No | Show full command line arguments. |
| Runtime | --logfile LOGFILE | No | Path to the log file. If not specified, messages will only be written to the standard error output. |
| Runtime | --tmp-dir TMP_DIR | No | Full path to the directory where temporary files will be stored. (default: .) |
| Runtime | --with-petagene-dir WITH_PETAGENE_DIR | No | 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. Optionally set the PetaLinkMode environment variable that is used to further configure PetaLink, notably setting it to "+write" to enable outputting compressed BAM and .fastq files. |
| Runtime | --keep-tmp | No | Do not delete the directory storing temporary files after completion. |
| Runtime | --no-seccomp-override | No | Do not override seccomp options for docker. |
| Runtime | --version | No | View compatible software versions. |
| Runtime | --preserve-file-symlinks | No | Override default behavior to keep file symlinks intact and *not* resolve the symlink. |
| Runtime | --num-gpus NUM_GPUS | No | Number of GPUs to use for a run. (default: 1) |