PICARD COLLECTINSERTSIZEMETRICS¶
Collect metrics on insert size of paired end reads with picard tools.
Software dependencies¶
- picard ==2.22.1
- r-base ==3.6.2
Example¶
This wrapper can be used in the following way:
rule insert_size:
input:
"mapped/{sample}.bam"
output:
txt="stats/{sample}.isize.txt",
pdf="stats/{sample}.isize.pdf"
log:
"logs/picard/insert_size/{sample}.log"
params:
# optional parameters (e.g. relax checks as below)
"VALIDATION_STRINGENCY=LENIENT "
"METRIC_ACCUMULATION_LEVEL=null "
"METRIC_ACCUMULATION_LEVEL=SAMPLE"
wrapper:
"0.59.1/bio/picard/collectinsertsizemetrics"
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__ = "johannes.koester@protonmail.com"
__license__ = "MIT"
from snakemake.shell import shell
log = snakemake.log_fmt_shell()
shell(
"picard CollectInsertSizeMetrics {snakemake.params} "
"INPUT={snakemake.input} OUTPUT={snakemake.output.txt} "
"HISTOGRAM_FILE={snakemake.output.pdf} {log}"
)