NVIDIA Clara Parabricks Pipelines:Variant Callers: CNVKIT

CPU accelerated Copy number variant calling


Run CNVkit with accelerated coverage calculation from read depths. CNVkit is not available as part of the free for Covid19 program.


Quick Start

CLI

$ pbrun cnvkit --ref Ref.fa \
--in-bam sample.bam
--out-file output.vcf


Options

Option

Description

--ref (required)

Path to the reference file.

--in-bam (required)

Path to the bam file.

--out-file

Path to the output vcf file.

--cnvkit-options

Pass supported cnvkit options as one string. e.g. --cnvkit-options="--count-reads --drop-low-coverage".

--generate-vcf

Export the output cns to vcf after running batch (default: None)