variantfiltration

Accelerated variant filtration based on conditions

Filter a vcf using a boolean expression.

Quick Start

CLI
$ 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

Options

Option

Description

--in-vcf (required)

Path to the input vcf file.

--out-file (required)

Path to the output variants file with an extension of either '.vcf' or '.csv'.

--expression (required)

Boolean expression for filtering variants.

--filter-name (required)

Field value for variants that pass the filter expression.

--mode

Defaults to BOTH.

Type of variants to include in the filter. Possible values are SNP, INDEL, orBOTH.