PICARD MARKDUPLICATES¶
Mark PCR and optical duplicates with picard tools.
Software dependencies¶
- picard ==2.9.2
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"
wrapper:
"0.35.2/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.
Authors¶
- Johannes Köster
Code¶
__author__ = "Johannes Köster"
__copyright__ = "Copyright 2016, Johannes Köster"
__email__ = "koester@jimmy.harvard.edu"
__license__ = "MIT"
from snakemake.shell import shell
shell("picard MarkDuplicates {snakemake.params} INPUT={snakemake.input} "
"OUTPUT={snakemake.output.bam} METRICS_FILE={snakemake.output.metrics} "
"&> {snakemake.log}")