Accelerated variant filtration based on conditions. Filters a VCF using a boolean expression. variantfiltration can only filter on INFO annotations, not on FORMAT.
$ pbrun variantfiltration \
--in-vcf sample.vcf \
--out-file output.vcf \
--expression "QD < 2.0 || ReadPosRankSum < -20.0" \
--filter-name FILTER
gatk VariantFiltration -V sample.vcf \
-O output.vcf \
--filter-expression "QD < 2.0 || ReadPosRankSum < -20.0" \
--filter-name FILTER
Filter a VCF using a boolean expression.
Input/Output file options
- --in-vcf IN_VCF
- --out-file OUT_FILE
Path to the input VCF file. (default: None)
Option is required.
Path to the output file with an extension of either '.vcf' or '.csv' (default: None)
Option is required.
Tool Options:
- -m MODE, --mode MODE Type of variants to include in the filter. Possible
- -e EXPRESSION, --expression EXPRESSION
- --filter-name FILTER_NAME
values are {SNP, INDEL, BOTH}. (default: BOTH)
Boolean expression for filtering variants (e.g. '--expression "QD < 2.0 || ReadPosRankSum < -20.0 || InbreedingCoeff < -0.8 || FS > 200.0"). (default: None)
Option is required.
Field value for variants that pass the filter expression. (default: None)
Option is required.
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.