GATK APPLYBQSR

Run gatk ApplyBQSR.

Software dependencies

• gatk4 ==4.1.4.1
• openjdk =8

Example

This wrapper can be used in the following way:

rule gatk_applybqsr:
    input:
        bam="mapped/{sample}.bam",
        ref="genome.fasta",
        dict="genome.dict",
        recal_table="recal/{sample}.grp"
    output:
        bam="recal/{sample}.bam"
    log:
        "logs/gatk/gatk_applybqsr/{sample}.log"
    params:
        extra="",  # optional
        java_opts="", # optional
    wrapper:
        "0.65.0/bio/gatk/applybqsr"

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. “-Xmx4G” for one, and “-Xmx4G -XX:ParallelGCThreads=10” for two options.
• The extra param allows for additional program arguments for ApplyBSQR.
• For more information see, https://gatk.broadinstitute.org/hc/en-us/articles/360037055712-ApplyBQSR

Authors

• Christopher Schröder
• Johannes Köster
• Jake VanCampen

Code

__author__ = "Christopher Schröder"
__copyright__ = "Copyright 2020, Christopher Schröder"
__email__ = "christopher.schroeder@tu-dortmund.de"
__license__ = "MIT"


from snakemake.shell import shell

extra = snakemake.params.get("extra", "")
java_opts = snakemake.params.get("java_opts", "")

log = snakemake.log_fmt_shell(stdout=True, stderr=True, append=True)
shell(
    "gatk --java-options '{java_opts}' ApplyBQSR {extra} -R {snakemake.input.ref} -I {snakemake.input.bam} "
    "--bqsr-recal-file {snakemake.input.recal_table} "
    "-O {snakemake.output.bam} {log}"
)