PICARD MARKDUPLICATES¶
Mark PCR and optical duplicates with picard tools. For more information about MarkDuplicates see picard documentation.
URL:
Example¶
This wrapper can be used in the following way:
rule mark_duplicates:
input:
"mapped/{sample}.bam"
# optional to specify a list of BAMs; this has the same effect
# of marking duplicates on separate read groups for a sample
# and then merging
output:
bam="dedup/{sample}.bam",
metrics="dedup/{sample}.metrics.txt"
log:
"logs/picard/dedup/{sample}.log"
params:
extra="REMOVE_DUPLICATES=true"
# optional specification of memory usage of the JVM that snakemake will respect with global
# resource restrictions (https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#resources)
# and which can be used to request RAM during cluster job submission as `{resources.mem_mb}`:
# https://snakemake.readthedocs.io/en/latest/executing/cluster.html#job-properties
resources:
mem_mb=1024
wrapper:
"0.80.1/bio/picard/markduplicates"
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¶
picard==2.22.1
snakemake-wrapper-utils==0.1.3
Authors¶
- Johannes Köster
Code¶
__author__ = "Johannes Köster"
__copyright__ = "Copyright 2016, Johannes Köster"
__email__ = "koester@jimmy.harvard.edu"
__license__ = "MIT"
from snakemake.shell import shell
from snakemake_wrapper_utils.java import get_java_opts
log = snakemake.log_fmt_shell(stdout=True, stderr=True)
extra = snakemake.params.get("extra", "")
java_opts = get_java_opts(snakemake)
bams = snakemake.input
if isinstance(bams, str):
bams = [bams]
bams = list(map("INPUT={}".format, bams))
shell(
"picard MarkDuplicates " # Tool and its subcommand
"{java_opts} " # Automatic java option
"{extra} " # User defined parmeters
"{bams} " # Input bam(s)
"OUTPUT={snakemake.output.bam} " # Output bam
"METRICS_FILE={snakemake.output.metrics} " # Output metrics
"{log}" # Logging
)