GATK LEARNREADORIENTATIONMODEL

Get the maximum likelihood estimates of artifact prior probabilities in the orientation bias mixture model filter

URL: https://gatk.broadinstitute.org/hc/en-us/articles/9570329571227-LearnReadOrientationModel

Example

This wrapper can be used in the following way:

rule test_gatk_learnreadorientationmodel:
    input:
        f1r2="f1r2.tar.gz",
    output:
        "artifacts_prior.tar.gz",
    resources:
        mem_mb=1024,
    params:
        extra="",
    log:
        "learnreadorientationbias.log",
    wrapper:
        "v4.6.0/bio/gatk/learnreadorientationmodel"

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=4.5.0.0
snakemake-wrapper-utils=0.6.2

Input/Output

Input:

f1r2: Path to one or multiple f1r2 files

Output:

Path to tar.gz of artifact prior tables

Authors

Thibault Dayris

Code

#!/usr/bin/env python3
# coding: utf-8

"""Snakemake wrapper for GATK4 LearnReadOrientationModel"""

__author__ = "Thibault Dayris"
__copyright__ = "Copyright 2022, Dayris Thibault"
__email__ = "thibault.dayris@gustaveroussy.fr"
__license__ = "MIT"

import tempfile
from snakemake.shell import shell
from snakemake_wrapper_utils.java import get_java_opts

log = snakemake.log_fmt_shell(stdout=True, stderr=True)
extra = snakemake.params.get("extra", "")
java_opts = get_java_opts(snakemake)

f1r2 = "--input "
if isinstance(snakemake.input["f1r2"], list):
    # Case user provided a list of archives
    f1r2 += "--input ".join(snakemake.input["f1r2"])
else:
    # Case user provided a single archive as a string
    f1r2 += snakemake.input["f1r2"]


with tempfile.TemporaryDirectory() as tmpdir:
    shell(
        "gatk --java-options '{java_opts}' LearnReadOrientationModel"  # Tool and its subprocess
        " {f1r2}"  # Path to input mapping file
        " {extra}"  # Extra parameters
        " --tmp-dir {tmpdir}"
        " --output {snakemake.output[0]}"  # Path to output vcf file
        " {log}"  # Logging behaviour
    )