GATK CALLCOPYRATIONSEGMENTS
Calls copy-ratio segments as amplified, deleted, or copy-number neutral
URL: https://gatk.broadinstitute.org/hc/en-us/articles/13832751795227-CallCopyRatioSegments
Example
This wrapper can be used in the following way:
rule call_copy_ratio_segments:
input:
copy_ratio_seg="a.cr.seg",
output:
called_copy_ratio_seg="a.called.seg",
igv_seg="a.called.igv.seg",
log:
"logs/gatk/call_copy_ratio_segments.log",
params:
#prefix="a.den.test",
extra="", # optional
java_opts="", # optional
resources:
mem_mb=1024,
wrapper:
"v3.9.0/bio/gatk/callcopyratiosegments"
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:
copy_ratio_seg
: cr.seq file from ModelSegments
Output:
copy_ratio_seg
: called copy ratio segments fileigv_seg
: CBS formatted igv.seg file, optional
Params
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).extra
: param allows for additional program arguments.
Code
__author__ = "Patrik Smeds"
__copyright__ = "Copyright 2023, Patrik Smed"
__email__ = "patrik.smeds@gmail.com"
__license__ = "MIT"
import os
import tempfile
from snakemake.shell import shell
from snakemake_wrapper_utils.java import get_java_opts
input_copy_ratio_seg = snakemake.input.copy_ratio_seg
called_copy_ratio_seg = snakemake.output.called_copy_ratio_seg
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:
outputfile_call = os.path.join(tmpdir, "temp.seq")
outputfile_igv = os.path.join(tmpdir, "temp.igv.seg")
shell(
"gatk --java-options '{java_opts}' CallCopyRatioSegments"
" -I {input_copy_ratio_seg}"
" -O {outputfile_call}"
" --tmp-dir {tmpdir}"
" {extra}"
" {log}"
)
shell("cp {outputfile_call} {called_copy_ratio_seg}")
if snakemake.output.get("igv_seg", None):
shell("cp {outputfile_igv} {snakemake.output.igv_seg}")