cnvkit

CPU accelerated Copy number variant calling. You need to pass "--extra-tools" to the installer to use this tool.

Run CNVkit with accelerated coverage calculation from read depths.

Quick Start

$ pbrun cnvkit \
    --ref Ref/Homo_sapiens_assembly38.fasta \
    --in-bam mark_dups_gpu.bam
    --output-dir outputFolder

cnvkit Reference

Calculate coverage from BAM read depths.

Input/Output file options

--ref REF

Path to the reference file. (default: None)

Option is required.

--in-bam IN_BAM

Path to the BAM file. (default: None)

Option is required.

--output-dir OUTPUT_DIR

Path to the directory that will contain all of the generated files. (default: None)

Option is required.

Options specific to this tool

--generate-vcf

Export the output CNS to VCF after running batch. (default: None)

--cnvkit-options CNVKIT_OPTIONS

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

(default: None)

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.