variantfiltration

Accelerated variant filtration based on conditions. Filters a VCF using a boolean expression. variantfiltration can only filter on INFO annotations, not on FORMAT.

Quick Start

$ pbrun variantfiltration \
    --in-vcf sample.vcf \
    --out-file output.vcf \
    --expression "QD < 2.0 || ReadPosRankSum < -20.0" \
    --filter-name FILTER

Compatible GATK4 Command

gatk VariantFiltration -V sample.vcf \
                       -O output.vcf \
                       --filter-expression "QD < 2.0 || ReadPosRankSum < -20.0" \
                       --filter-name FILTER

variantfiltration Reference

Filter a VCF using a boolean expression.

Input/Output file options

--in-vcf IN_VCF

Path to the input VCF file. (default: None)

Option is required.

--out-file OUT_FILE

Path to the output file with an extension of either '.vcf' or '.csv' (default: None)

Option is required.

Options specific to this tool

-m MODE, --mode MODE Type of variants to include in the filter. Possible

values are {SNP, INDEL, BOTH}. (default: BOTH)

-e EXPRESSION, --expression EXPRESSION

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.

--filter-name FILTER_NAME

Field value for variants that pass the filter expression. (default: None)

Option is required.

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.