GATK DENOISEREADCOUNTS
Denoises read counts to produce denoised copy ratios
URL: https://gatk.broadinstitute.org/hc/en-us/articles/13832751133851-DenoiseReadCounts
Example
This wrapper can be used in the following way:
rule denoisereadcounts:
input:
hdf5=["a.counts.hdf5"],
output:
std_copy_ratio="a.standardizedCR.tsv",
denoised_copy_ratio="a.denoisedCR.tsv",
log:
"logs/gatk/denoisereadcounts.log",
params:
extra="", # optional
java_opts="", # optional
resources:
mem_mb=1024,
wrapper:
"v3.9.0/bio/gatk/denoisereadcounts"
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
gatk4=4.5.0.0
snakemake-wrapper-utils=0.6.2
Input/Output
Input:
hdf5
: TSV or HDF5 file with counts from CollectReadCounts.pon
: Panel-of-normals from CreateReadCountPanelOfNormals (optional)gc_interval
: GC-content annotated-intervals from {@link AnnotateIntervals (optional)
Output:
std_copy_ratio
: Standardized-copy-ratios filedenoised_copy_ratio
: Denoised-copy-ratios file
Params
java_opts
: 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).extra
: additional program arguments.
Code
__author__ = "Patrik Smeds"
__copyright__ = "Copyright 2023, Patrik Smed"
__email__ = "patrik.smeds@gmail.com"
__license__ = "MIT"
import tempfile
from snakemake.shell import shell
from snakemake_wrapper_utils.java import get_java_opts
pon = snakemake.input.get("pon", "")
if pon:
pon = f"--count-panel-of-normals {snakemake.input.pon}"
gc_interval = snakemake.input.get("gc_interval", "")
if gc_interval:
gc_interval = f"--annotated-intervals {snakemake.input.gc_interval}"
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}' DenoiseReadCounts"
" --input {snakemake.input.hdf5}"
" {pon}"
" {gc_interval}"
" {extra}"
" --standardized-copy-ratios {snakemake.output.std_copy_ratio}"
" --denoised-copy-ratios {snakemake.output.denoised_copy_ratio}"
" --tmp-dir {tmpdir}"
" {log}"
)