PICARD COLLECTINSERTSIZEMETRICS
Collect metrics on insert size of paired end reads with picard tools.
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)
extra="--VALIDATION_STRINGENCY LENIENT --METRIC_ACCUMULATION_LEVEL null --METRIC_ACCUMULATION_LEVEL SAMPLE",
# 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:
"v5.0.1/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.
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#CollectInsertSizeMetrics
Software dependencies
picard=3.3.0
r-base=4.4.1
snakemake-wrapper-utils=0.6.2
Input/Output
Input:
bam file
Output:
txt
: textual representation of metricspdf
: insert size histogram
Code
__author__ = "Johannes Köster"
__copyright__ = "Copyright 2016, Johannes Köster"
__email__ = "johannes.koester@protonmail.com"
__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)
with tempfile.TemporaryDirectory() as tmpdir:
shell(
"picard CollectInsertSizeMetrics"
" {java_opts} {extra}"
" --INPUT {snakemake.input}"
" --TMP_DIR {tmpdir}"
" --OUTPUT {snakemake.output.txt}"
" --Histogram_FILE {snakemake.output.pdf}"
" {log}"
)