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:
        "v3.9.0-14-g476823b/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 file

• igv_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.

Authors

• Patrik Smeds

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}")