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.
# 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
- --in-pon-file IN_PON_FILE
- --out-vcf OUT_VCF
Path to the input vcf file. (default: None)
Option is required.
Path to the input PON file in vcf.gz format with its tabix index. (default: None)
Option is required.
Output annotated VCF file. (default: None)
Option is required.
Options specific to this tool
(none)
Common options:
- --logfile LOGFILE
- --tmp-dir TMP_DIR
- --with-petagene-dir WITH_PETAGENE_DIR
- --keep-tmp
- --no-seccomp-override
- --version
Path to the log file. If not specified, messages will only be written to the standard error output. (default: None)
Full path to the directory where temporary files will be stored.
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)
Do not delete the directory storing temporary files after completion.
Do not override seccomp options for docker (default: None).
View compatible software versions.