GATK APPLYBQSR¶
Run gatk ApplyBQSR.
URL:
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
resources:
mem_mb=1024
wrapper:
"v1.1.0/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.
Software dependencies¶
gatk4==4.1.4.1
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 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
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, 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}"
)