DELLY¶
Call variants with delly.
URL:
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:
"0.80.2/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}"
)