GATK BASERECALIBRATOR
Run gatk BaseRecalibrator.
URL: https://gatk.broadinstitute.org/hc/en-us/articles/9570376886683-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
resources:
mem_mb=1024,
wrapper:
"v5.0.0/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.
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.
Software dependencies
gatk4=4.6.1.0
snakemake-wrapper-utils=0.6.2
Input/Output
Input:
bam file
fasta reference
vcf.gz of known variants
Output:
recalibration table for the bam
Code
__author__ = "Christopher Schröder"
__copyright__ = "Copyright 2020, Christopher Schröder"
__email__ = "christopher.schroeder@tu-dortmund.de"
__license__ = "MIT"
import tempfile
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))
with tempfile.TemporaryDirectory() as tmpdir:
shell(
"gatk --java-options '{java_opts}' BaseRecalibrator"
" --input {snakemake.input.bam}"
" --reference {snakemake.input.ref}"
" {known}"
" {extra}"
" --tmp-dir {tmpdir}"
" --output {snakemake.output.recal_table}"
" {log}"
)