GATK APPLYBQSR¶
Run gatk ApplyBQSR.
URL: https://gatk.broadinstitute.org/hc/en-us/articles/9570337264923-ApplyBQSR
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
embed_ref=True, # embed the reference in cram output
resources:
mem_mb=1024,
wrapper:
"v1.21.1/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.
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=4.3.0.0
snakemake-wrapper-utils=0.5.0
samtools=1.16.1
Input/Output¶
Input:
- BAM file
- FASTA reference
- recalibration table for the bam
Output:
- recalibrated bam file
Authors¶
- Christopher Schröder
- Johannes Köster
- Jake VanCampen
- Filipe G. Vieira
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
# Extract arguments
extra = snakemake.params.get("extra", "")
reference = snakemake.input.get("ref")
embed_ref = snakemake.params.get("embed_ref", False)
java_opts = get_java_opts(snakemake)
log = snakemake.log_fmt_shell(stdout=True, stderr=True, append=True)
if snakemake.output.bam.endswith(".cram") and embed_ref:
output = "/dev/stdout"
pipe_cmd = " | samtools view -h -O cram,embed_ref -T {reference} -o {snakemake.output.bam} -"
else:
output = snakemake.output.bam
pipe_cmd = ""
with tempfile.TemporaryDirectory() as tmpdir:
shell(
"(gatk --java-options '{java_opts}' ApplyBQSR"
" --input {snakemake.input.bam}"
" --bqsr-recal-file {snakemake.input.recal_table}"
" --reference {reference}"
" {extra}"
" --tmp-dir {tmpdir}"
" --output {output}" + pipe_cmd + ") {log}"
)