Generate a index for a PON file. This is a prerequisite for calling "--pon" during mutect.
$ pbrun prepon \ --in-pon-file pon.vcf.gz
Build the index for a PON file; this is a prerequisite for mutect pon
Input/Output file options¶
- --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.
Options specific to this tool¶
- --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)
Do not delete the directory storing temporary files after completion.
- --license-file LICENSE_FILE
Path to license file license.bin if not in the installation directory.
Do not override seccomp options for docker (default: None).
View compatible software versions.