GATK BASERECALIBRATORSPARK

Run gatk BaseRecalibratorSpark.

Software dependencies

• gatk4 ==4.1.4.1
• openjdk =8

Example

This wrapper can be used in the following way:

rule gatk_baserecalibratorspark:
    input:
        bam="mapped/{sample}.bam",
        ref="genome.fasta",
        dict="genome.dict",
        known="dbsnp.vcf.gz"  # optional known sites
    output:
        recal_table="recal/{sample}.grp"
    log:
        "logs/gatk/baserecalibrator/{sample}.log"
    params:
        extra="",  # optional
        java_opts="", # optional
        #spark_runner="",  # optional, local by default
        #spark_0.67.0="",  # optional
        #spark_extra="", # optional
    threads: 8
    wrapper:
        "0.67.0/bio/gatk/baserecalibratorspark"

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 baserecalibratorspark.
• The spark_runner param = “LOCAL”|”SPARK”|”GCS” allows to set the spark_runner. Set the parameter to “LOCAL” or don’t set it at all to run on local machine.
• The spark_master param allows to set the URL of the Spark Master to submit the job. Set to “local[number_of_cores]” for local execution. Don’t set it at all for local execution with number of cores determined by snakemake.
• The ‘spark_extra’ param allows for additional spark arguments.
• For more information see, https://gatk.broadinstitute.org/hc/en-us/articles/360036897372-BaseRecalibratorSpark-BETA-

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", "")
spark_runner = snakemake.params.get("spark_runner", "LOCAL")
spark_master = snakemake.params.get(
    "spark_master", "local[{}]".format(snakemake.threads)
)
spark_extra = snakemake.params.get("spark_extra", "")
java_opts = snakemake.params.get("java_opts", "")

log = snakemake.log_fmt_shell(stdout=True, stderr=True)
known = snakemake.input.get("known", "")
if known:
    known = "--known-sites {}".format(known)

shell(
    "gatk --java-options '{java_opts}' BaseRecalibratorSpark {extra} "
    "-R {snakemake.input.ref} -I {snakemake.input.bam} "
    "-O {snakemake.output.recal_table} {known} "
    "-- --spark-runner {spark_runner} --spark-master {spark_master} {spark_extra} "
    "{log}"
)