GATK SCATTERINTERVALSBYNS
Run gatk ScatterIntervalsByNs.
URL: https://gatk.broadinstitute.org/hc/en-us/articles/9570421542811-ScatterIntervalsByNs-Picard-
Example
This wrapper can be used in the following way:
rule gatk_scatter_interval_by_ns:
input:
ref="genome.fasta",
fai="genome.fasta.fai",
dict="genome.dict",
output:
intervals="genome.intervals",
log:
"logs/genome.log",
params:
extra="--MAX_TO_MERGE 10 --OUTPUT_TYPE ACGT",
java_opts="", # optional
resources:
mem_mb=1024,
wrapper:
"v5.0.0/bio/gatk/scatterintervalsbyns"
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.
Software dependencies
gatk4=4.6.1.0
snakemake-wrapper-utils=0.6.2
Input/Output
Input:
reference genome
Output:
interval list
Code
__author__ = "Filipe G. Vieira"
__copyright__ = "Copyright 2021, Filipe G. Vieira"
__license__ = "MIT"
import tempfile
from snakemake.shell import shell
from snakemake_wrapper_utils.java import get_java_opts
extra = snakemake.params.get("extra", "")
java_opts = get_java_opts(snakemake)
log = snakemake.log_fmt_shell(stdout=True, stderr=True)
with tempfile.TemporaryDirectory() as tmpdir:
shell(
"gatk --java-options '{java_opts}' ScatterIntervalsByNs"
" --REFERENCE {snakemake.input.ref}"
" {extra}"
" --TMP_DIR {tmpdir}"
" --OUTPUT {snakemake.output.intervals}"
" {log}"
)