DELLY

Call variants with delly.

Software dependencies

• delly ==0.7.7

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/{type,(DEL|DUP|INV|TRA|INS)}.bcf"
    params:
        vartype="{type}", # variant type to call (can be wildcard, hardcoded string or function)
        extra=""  # optional parameters for delly (except -t, -g)
    log:
        "logs/delly/{type}.log"
    threads: 3
    wrapper:
        "0.19.1/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.

Authors

• Johannes Köster

Code

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


from snakemake.shell import shell


try:
    exclude = "-x " + snakemake.input.exclude
except AttributeError:
    exclude = ""


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

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