GATK BASERECALIBRATOR¶
Run gatk BaseRecalibrator.
Example¶
This wrapper can be used in the following way:
rule gatk_baserecalibrator:
input:
bam="mapped/{sample}.bam",
ref="genome.fasta",
dict="genome.dict",
known="dbsnp.vcf.gz" # optional known sites - single or a list
output:
recal_table="recal/{sample}.grp"
log:
"logs/gatk/baserecalibrator/{sample}.log"
params:
extra="", # optional
java_opts="", # optional
# optional specification of memory usage of the JVM that snakemake will respect with global
# resource restrictions (https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#resources)
# and which can be used to request RAM during cluster job submission as `{resources.mem_mb}`:
# https://snakemake.readthedocs.io/en/latest/executing/cluster.html#job-properties
resources:
mem_mb=1024
wrapper:
"0.76.0/bio/gatk/baserecalibrator"
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
- vcf.gz of known variants
Output:
- recalibration table for the bam
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 more information see, https://software.broadinstitute.org/gatk/documentation/article?id=11050
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)
known = snakemake.input.get("known", "")
if known:
if isinstance(known, str):
known = [known]
known = list(map("--known-sites {}".format, known))
shell(
"gatk --java-options '{java_opts}' BaseRecalibrator {extra} "
"-R {snakemake.input.ref} -I {snakemake.input.bam} "
"-O {snakemake.output.recal_table} {known} {log}"
)