PICARD MARKDUPLICATESWITHMATECIGAR¶
Mark PCR and optical duplicates with picard tools, taking into account the CIGAR of the mate.
URL:
Example¶
This wrapper can be used in the following way:
rule mark_duplicates:
input:
"mapped/{sample}.bam"
output:
bam="dedup/{sample}.bam",
metrics="dedup/{sample}.metrics.txt"
log:
"logs/picard/dedup/{sample}.log"
params:
"REMOVE_DUPLICATES=true"
resources:
mem_mb=1024
wrapper:
"v0.80.1/bio/picard/markduplicateswithmatecigar"
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
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.
- For more information see, https://broadinstitute.github.io/picard/command-line-overview.html#MarkDuplicatesWithMateCigar
Authors¶
- Johannes Köster
- Filipe G. Vieira
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, append=True)
extra = snakemake.params.get("extra", "")
java_opts = get_java_opts(snakemake)
shell(
"picard MarkDuplicatesWithMateCigar {java_opts} {extra} INPUT={snakemake.input} "
"OUTPUT={snakemake.output.bam} METRICS_FILE={snakemake.output.metrics} "
"{log}"
)