cnvkit

Accelerated CNVkit. Currently we support three CNVkit sub-commands: batch, autobin and coverage. The help below is divided into a section for options common to all subcommands, followed by options for the batch, autobin and coverage subcommands.

--ref REF

Path to the reference file. (default: None)

--in-bam IN_BAM

Path to the BAM file. (default: None)

Option is required.

(none)

--sub-command SUB_COMMAND

The sub-command to call in CNVkit tool. Value can be one of [batch, autobin, coverage]. (default: None)

--batch-output-dir BATCH_OUTPUT_DIR

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

--batch-access BATCH_ACCESS

Regions of accessible sequence on chromosomes (.bed) (default: None)

--batch-targets BATCH_TARGETS

Target intervals (.bed or .list) (default: None)

--batch-annotate BATCH_ANNOTATE

Use gene models from this file to assign names to the target regions. Format: UCSC refFlat.txt or ensFlat.txt file (preferred), or BED, interval list, GFF, or similar. (default: None)

--batch-cnn-reference BATCH_CNN_REFERENCE

Copy number reference file (.cnn), to reuse an existing reference (default: None)

--generate-vcf

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

--batch-cnvkit-options BATCH_CNVKIT_OPTIONS

Pass supported batch CNVkit options as one string (e.g. --batch-cnvkit-options="--count-reads --drop-low-coverage --target-avg-size 5000 ") (default: None)

--autobin-access AUTOBIN_ACCESS

Sequencing-accessible genomic regions, or exons to use as possible targets. (default: None)

--autobin-targets AUTOBIN_TARGETS

Potentially targeted genomic regions, e.g. all possible exons for the reference genome. Format: BED, interval list, etc. (default: None)

--autobin-annotate AUTOBIN_ANNOTATE

Use gene models from this file to assign names to the target regions. Format: UCSC refFlat.txt or ensFlat.txt file (preferred), or BED, interval list, GFF, or similar. (default: None)

--target-output-bed TARGET_OUTPUT_BED

Filename for target BED output. (default: None)

--antitarget-output-bed ANTITARGET_OUTPUT_BED

Filename for antitarget BED output. (default: None)

--bp-per-bin BP_PER_BIN

Desired average number of sequencing read bases mapped to each bin. (default: 100000.0)

--target-max-size TARGET_MAX_SIZE

Maximum size of target bins. (default: 20000)

--target-min-size TARGET_MIN_SIZE

Minimum size of target bins. (default: 20)

--antitarget-max-size ANTITARGET_MAX_SIZE

Maximum size of antitarget bins. (default: 500000)

--antitarget-min-size ANTITARGET_MIN_SIZE

Minimum size of antitarget bins. (default: 500)

--short-names

Reduce multi-accession bait labels to be short and consistent. (default: None)

--coverage-output COVERAGE_OUTPUT

Output file name of coverage. (default: None)

--coverage-interval COVERAGE_INTERVAL

Input interval file name of coverage. (default: None)

--count

Get read depths by counting read midpoints within each bin (an alternative algorithm). (default: None)

--processes PROCESSES

Number of subprocesses to calculate coverage in parallel. (default: 4)

--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.