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:
"v1.3.1/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=2.26
snakemake-wrapper-utils==0.1.3
Notes¶
- The java_opts param allows for additional arguments to be passed to the java compiler, e.g. “-XX:ParallelGCThreads=10” (not for -XmX or -Djava.io.tmpdir, since they are handled automatically).
- The extra param allows for additional program arguments.
- –TMP_DIR is automatically set by resources.tmpdir
- For more information see, https://broadinstitute.github.io/picard/command-line-overview.html#MarkDuplicates
Authors¶
- Johannes Köster
Code¶
__author__ = "Johannes Köster"
__copyright__ = "Copyright 2016, Johannes Köster"
__email__ = "koester@jimmy.harvard.edu"
__license__ = "MIT"
import tempfile
from snakemake.shell import shell
from snakemake_wrapper_utils.java import get_java_opts
log = snakemake.log_fmt_shell()
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))
with tempfile.TemporaryDirectory() as tmpdir:
shell(
"picard MarkDuplicates" # Tool and its subcommand
" {java_opts}" # Automatic java option
" {extra}" # User defined parmeters
" {bams}" # Input bam(s)
" --TMP_DIR {tmpdir}"
" --OUTPUT {snakemake.output.bam}" # Output bam
" --METRICS_FILE {snakemake.output.metrics}" # Output metrics
" {log}" # Logging
)