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.
# 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:4.4.0-1 \
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.
GPU options:
- --num-gpus NUM_GPUS
-
Number of GPUs to use for a run. GPUs 0..(NUM_GPUS-1) will be used.