prepon
Generate an index for a PON file. This is a prerequisite for using the "--pon" option in mutectcaller.
prepon requires that the Contig field be present in the header of the input .vcf.gz file in order to do
memory allocation at the start of execution. This field should include both the chromosome name and length:
##contig=<ID=chr1,length=248956422>
##contig=<ID=chr2,length=242193529>
##contig=<ID=chr3,length=198295559>
...
If your input .vcf.gz file does not include these value, run this command to update the header before running prepon:
$ bcftools reheader --fai YOUR_REFERENCE_FILE.fa.fai INPUT_PON.vcf.gz > UPDATED_PON.vcf.gz
See the prepon Reference section for a detailed listing of all available options.
# This command assumes all the inputs are in the current working directory and all the outputs go to the same place.
docker run --rm --gpus all --volume $(pwd):/workdir --volume $(pwd):/outputdir \
--workdir /workdir \
nvcr.io/nvidia/clara/clara-parabricks:4.5.1-1 \
pbrun prepon \
--in-pon-file /workdir/${INPUT_PON_VCF}
Build the index for a PON file; this is a prerequisite for mutect PON.
Type | Name | Required? | Description |
|---|---|---|---|
| I/O | ‑‑in‑pon‑file IN_PON_FILE | Yes | Path to the input PON file in vcf.gz format with its tabix index. |
| 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 | ‑‑num‑gpus NUM_GPUS | No | Number of GPUs to use for a run. (default: 1) |