frequencyfiltration
Filter variants within a VCF file by numeric fields containing frequency/count information.
$ pbrun frequencyfiltration \
--in-vcf input.vcf \
--out-vcf output.vcf \
--or-expression "gnomad_AF <= 0.02" \
--or-expression "dbsnpCOMMON != 1"
Filter variants within a VCF file by numeric fields.
Input/Output file options
- --in-vcf IN_VCF
- --out-vcf OUT_VCF
- --excluded-vcf EXCLUDED_VCF
Path to the input VCF file to filter. (default: None)
Option is required.
Path to the output filtered VCF file. (default: None)
Option is required.
A path to write variants which fail filtration.
(default: None)
Options specific to this tool
- --and-expression AND_EXPRESSION
- --or-expression OR_EXPRESSION
- --drop-missing
A string of the form "VARIABLE OPERATOR THRESHOLD" to use for filtering (e.g. "AF < 0.02"). A variant must pass all AND expressions to pass filtering. (default: None)
A string of the form "VARIABLE OPERATOR THRESHOLD" to use for filtering (e.g. "AF < 0.02"). A variant need only pass a single OR expression to pass filtering. (default: None)
Drop variants that are missing any fields used in filtering expressions from output. (default: None)
Common options:
- --logfile LOGFILE
- --tmp-dir TMP_DIR
- --with-petagene-dir WITH_PETAGENE_DIR
- --keep-tmp
- --license-file LICENSE_FILE
- --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.
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.