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:
"0.71.0/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.
Software dependencies¶
picard==2.22.1
snakemake-wrapper-utils==0.1.3
Authors¶
- Julian de Ruiter
Code¶
"""Snakemake wrapper for picard CollectHSMetrics."""
__author__ = "Julian de Ruiter"
__copyright__ = "Copyright 2017, Julian de Ruiter"
__email__ = "julianderuiter@gmail.com"
__license__ = "MIT"
from snakemake.shell import shell
from snakemake_wrapper_utils.java import get_java_opts
inputs = " ".join("INPUT={}".format(in_) for in_ in snakemake.input)
extra = snakemake.params.get("extra", "")
log = snakemake.log_fmt_shell(stdout=False, stderr=True)
java_opts = get_java_opts(snakemake)
shell(
"picard CollectHsMetrics"
" {java_opts} {extra}"
" INPUT={snakemake.input.bam}"
" OUTPUT={snakemake.output[0]}"
" REFERENCE_SEQUENCE={snakemake.input.reference}"
" BAIT_INTERVALS={snakemake.input.bait_intervals}"
" TARGET_INTERVALS={snakemake.input.target_intervals}"
" {log}"
)