NVIDIA Clara Parabricks Pipelines:Variant Processing: 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
Path to the input vcf file.
Path to the output variants file with an extension of either '.vcf' or '.csv'.
Boolean expression for filtering variants.
Field value for variants that pass the filter expression.
Defaults to BOTH.
Type of variants to include in the filter. Possible values are SNP, INDEL, orBOTH.