DELLY

Call variants with delly.

Example

This wrapper can be used in the following way:

rule delly:
    input:
        ref="genome.fasta",
        samples=["mapped/a.bam"],
        # optional exclude template (see https://github.com/dellytools/delly)
        exclude="human.hg19.excl.tsv"
    output:
        "sv/calls.bcf"
    params:
        extra=""  # optional parameters for delly (except -g, -x)
    log:
        "logs/delly.log"
    threads: 2  # It is best to use as many threads as samples
    wrapper:
        "0.75.0-7-g74e079c/bio/delly"

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

  • delly==0.8.7

Authors

  • Johannes Köster

Code

__author__ = "Johannes Köster"
__copyright__ = "Copyright 2016, Johannes Köster"
__email__ = "koester@jimmy.harvard.edu"
__license__ = "MIT"


from snakemake.shell import shell


exclude = (
    "-x {}".format(snakemake.input.exclude)
    if snakemake.input.get("exclude", "")
    else ""
)

extra = snakemake.params.get("extra", "")
log = snakemake.log_fmt_shell(stdout=True, stderr=True)

shell(
    "OMP_NUM_THREADS={snakemake.threads} delly call {extra} "
    "{exclude} -g {snakemake.input.ref} "
    "-o {snakemake.output[0]} {snakemake.input.samples} {log}"
)