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.
$ pbrun cnvkit \
--ref Ref/Homo_sapiens_assembly38.fasta \
--in-bam mark_dups_gpu.bam
--output-dir outputFolder
Calculate coverage from BAM read depths.
Input/Output file options
- --ref REF
- --in-bam IN_BAM
- --output-dir OUTPUT_DIR
Path to the reference file. (default: None)
Option is required.
Path to the BAM file. (default: None)
Option is required.
Path to the directory that will contain all of the generated files. (default: None)
Option is required.
Options specific to this tool
- --generate-vcf
- --cnvkit-options CNVKIT_OPTIONS
Export the output CNS to VCF after running batch. (default: None)
Pass supported cnvkit options as one string. e.g. --cnvkit-options="--count-reads --drop-low-coverage"
(default: None)
Common options:
- --logfile LOGFILE
- --tmp-dir TMP_DIR
- --with-petagene-dir WITH_PETAGENE_DIR
- --keep-tmp
- --license-file LICENSE_FILE
- --no-seccomp-override
- --version
Path to the log file. If not specified, messages will only be written to the standard error output. (default: None)
Full path to the directory where temporary files will be stored.
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)
Do not delete the directory storing temporary files after completion.
Path to license file license.bin if not in the installation directory.
Do not override seccomp options for docker (default: None).
View compatible software versions.