cnvkit

CPU accelerated Copy number variant calling

Run CNVkit with accelerated coverage calculation from read depths.

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".