GATK APPLYBQSRSPARK¶
ApplyBQSRSpark: Apply base quality score recalibration on Spark; uses output of the BaseRecalibrator tool.
URL:
Example¶
This wrapper can be used in the following way:
rule gatk_applybqsr_spark:
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_spark/{sample}.log"
params:
extra="", # optional
java_opts="", # optional
#spark_runner="", # optional, local by default
#spark_v0.80.1="", # optional
#spark_extra="", # optional
resources:
mem_mb=1024
wrapper:
"v0.80.1/bio/gatk/applybqsrspark"
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
openjdk=8
snakemake-wrapper-utils=0.1.3
Input/Output¶
Input:
- bam file
- fasta reference
- recalibration table for the bam
Output:
- recalibrated bam 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 applybqsrspark.
- 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/360057440431-ApplyBQSRSpark-BETA-
Authors¶
- Filipe G. Vieira
Code¶
__author__ = "Filipe G. Vieira"
__copyright__ = "Copyright 2021, Filipe G. Vieira"
__license__ = "MIT"
import tempfile
from snakemake.shell import shell
from snakemake_wrapper_utils.java import get_java_opts
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 = get_java_opts(snakemake)
tmpdir = tempfile.gettempdir()
log = snakemake.log_fmt_shell(stdout=True, stderr=True)
shell(
"gatk --java-options '{java_opts}' ApplyBQSRSpark {extra} "
"--reference {snakemake.input.ref} --input {snakemake.input.bam} "
"--bqsr-recal-file {snakemake.input.recal_table} "
"--tmp-dir {tmpdir} "
"--output {snakemake.output.bam} "
"-- --spark-runner {spark_runner} --spark-master {spark_master} {spark_extra} "
"{log}"
)