GATK CLEANSAM

Run gatk CleanSam

URL:

Example

This wrapper can be used in the following way:

rule gatk_clean_sam:
    input:
        bam="{sample}.bam"
    output:
        clean="{sample}.clean.bam"
    log:
        "logs/{sample}.log"
    params:
        extra="",
    java_opts="", # optional
    resources:
        mem_mb=1024,
    wrapper:
        "v1.1.0/bio/gatk/cleansam"

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==4.2.0.0
• snakemake-wrapper-utils==0.1.3

Input/Output

Input:

• SAM/BAM/CRAM file

Output:

• clean and validates SAM/BAM/CRAM file

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.
• For more information see, https://gatk.broadinstitute.org/hc/en-us/articles/360056970832-CleanSam-Picard-

Authors

• Filipe G. Vieira

Code

__author__ = "Filipe G. Vieira"
__copyright__ = "Copyright 2021, Filipe G. Vieira"
__license__ = "MIT"


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)
shell(
    "gatk --java-options '{java_opts}' CleanSam --INPUT {snakemake.input.bam} "
    "{extra} --OUTPUT {snakemake.output.clean} {log}"
)