CNVKIT TARGET

Prepare a BED file of baited regions for use with CNVkit.

URL: https://cnvkit.readthedocs.io/en/stable/pipeline.html#target

Example

This wrapper can be used in the following way:

rule cnvkit_targetl:
    input:
        bed="test.bed",
        annotate="refflat-mini.txt",
    output:
        bed="test.target.bed",
    log:
        "logs/test.target.log",
    params:
        extra = "--split" # optional
    wrapper:
        "v3.9.0-14-g476823b/bio/cnvkit/target"

Note that input, output and log file paths can be chosen freely.

When running with

snakemake --use-conda

the software dependencies will be automatically deployed into an isolated environment before execution.

Software dependencies

• cnvkit=0.9.11

Input/Output

Input:

• bed: bed file

• annotate: gene annotation databases, e.g. RefSeq or Ensembl, as a “flat” format (can be found at UCSC) (optional)

Output:

• bed: bed file

Params

• extra: additional parameters that will be forwarded to cnvkit target

Authors

• Patrik Smeds

Code

__author__ = "Patrik Smeds"
__copyright__ = "Copyright 2023, Patrik Smeds"
__email__ = "patrik.smeds@gmail.com"
__license__ = "MIT"

from snakemake.shell import shell

log = snakemake.log_fmt_shell(stdout=False, stderr=True)

extra = snakemake.params.get("extra", "")

annotate = snakemake.input.get("annotate", "")
if annotate:
    annotate = f"--annotate {annotate}"

shell(
    "cnvkit.py target "
    "{snakemake.input.bed} "
    "-o {snakemake.output.bed} "
    "{annotate} "
    "{extra} "
    "{log}"
)