PICARD COLLECTHSMETRICS
Collects hybrid-selection (HS) metrics for a SAM or BAM file using picard.
Example
This wrapper can be used in the following way:
rule picard_collect_hs_metrics:
input:
bam="mapped/{sample}.bam",
reference="genome.fasta",
# Baits and targets should be given as interval lists. These can
# be generated from bed files using picard BedToIntervalList.
bait_intervals="regions.intervals",
target_intervals="regions.intervals",
output:
"stats/hs_metrics/{sample}.txt",
params:
# Optional extra arguments. Here we reduce sample size
# to reduce the runtime in our unit test.
extra="--SAMPLE_SIZE 1000",
# 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,
log:
"logs/picard_collect_hs_metrics/{sample}.log",
wrapper:
"v5.8.0/bio/picard/collecthsmetrics"
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#CollectHSMetrics
Software dependencies
picard=3.3.0
snakemake-wrapper-utils=0.6.2
Input/Output
Input:
bam file
Output:
metrics file
Code
"""Snakemake wrapper for picard CollectHSMetrics."""
__author__ = "Julian de Ruiter"
__copyright__ = "Copyright 2017, Julian de Ruiter"
__email__ = "julianderuiter@gmail.com"
__license__ = "MIT"
import tempfile
from snakemake.shell import shell
from snakemake_wrapper_utils.java import get_java_opts
log = snakemake.log_fmt_shell(stdout=False, stderr=True)
extra = snakemake.params.get("extra", "")
java_opts = get_java_opts(snakemake)
with tempfile.TemporaryDirectory() as tmpdir:
shell(
"picard CollectHsMetrics"
" {java_opts} {extra}"
" --INPUT {snakemake.input.bam}"
" --TMP_DIR {tmpdir}"
" --OUTPUT {snakemake.output[0]}"
" --REFERENCE_SEQUENCE {snakemake.input.reference}"
" --BAIT_INTERVALS {snakemake.input.bait_intervals}"
" --TARGET_INTERVALS {snakemake.input.target_intervals}"
" {log}"
)