postpon

Annotate variants based on a PON file and modify the "INFO" field of input VCF file. This is the post process of calling "--pon" in mutect.

Quick Start

$ pbrun postpon \
    --in-vcf input.vcf \
    --in-pon-file pon.vcf.gz \
    --out-vcf output.vcf

postpon Reference

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.

--license-file LICENSE_FILE

Path to license file license.bin if not in the installation directory.

--no-seccomp-override

Do not override seccomp options for docker (default: None).

--version

View compatible software versions.