SAMBAMBA MARKDUP
Marks (default) or removes duplicate reads in BAM file. See details `here https://lomereiter.github.io/sambamba/docs/sambamba-markdup.html`_
Example
This wrapper can be used in the following way:
rule sambamba_markdup:
input:
"mapped/{sample}.bam"
output:
"mapped/{sample}.rmdup.bam"
params:
extra="-r" # optional parameters
log:
"logs/sambamba-markdup/{sample}.log"
threads: 8
wrapper:
"v5.8.0/bio/sambamba/markdup"
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
sambamba=1.0.1
Input/Output
Input:
bam file
Output:
deduplicated bam file
Code
__author__ = "Jan Forster"
__copyright__ = "Copyright 2021, Jan Forster"
__email__ = "j.forster@dkfz.de"
__license__ = "MIT"
import os
from snakemake.shell import shell
from tempfile import TemporaryDirectory
log = snakemake.log_fmt_shell(stdout=True, stderr=True)
with TemporaryDirectory() as tempdir:
shell(
"sambamba markdup {snakemake.params.extra} --nthreads {snakemake.threads} "
"--tmpdir {tempdir} {snakemake.input[0]} {snakemake.output[0]} "
"{log}"
)