GATK3 BASERECALIBRATOR¶
Run gatk3 BaseRecalibrator.
URL:
Example¶
This wrapper can be used in the following way:
rule baserecalibrator:
input:
bam="mapped/{sample}.bam",
ref="genome.fasta",
known="dbsnp.vcf.gz"
output:
"{sample}.recal_data_table"
log:
"logs/gatk3/bqsr/{sample}.log"
params:
extra="" # optional
resources:
mem_mb = 1024
threads: 16
wrapper:
"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¶
gatk==3.8
snakemake-wrapper-utils==0.1.3
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
- Gatk3.jar is not included in the bioconda package, i.e it need to be added to the conda environment manually.
Authors¶
- Patrik Smeds
Code¶
__author__ = "Patrik Smeds"
__copyright__ = "Copyright 2019, Patrik Smeds"
__email__ = "patrik.smeds@gmail.com.com"
__license__ = "MIT"
import os
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)
input_bam = snakemake.input.bam
input_known = snakemake.input.known
input_ref = snakemake.input.ref
bed = snakemake.params.get("bed", None)
if bed is not None:
bed = "-L " + bed
else:
bed = ""
input_known_string = ""
for known in input_known:
input_known_string = input_known_string + " --knownSites {}".format(known)
log = snakemake.log_fmt_shell(stdout=True, stderr=True)
shell(
"gatk3 {java_opts} -T BaseRecalibrator"
" -nct {snakemake.threads}"
" {extra}"
" -I {input_bam}"
" -R {input_ref}"
" {input_known_string}"
" {bed}"
" -o {snakemake.output}"
" {log}"
)