GATK3 BASERECALIBRATOR¶
Run gatk3 BaseRecalibrator.
Example¶
This wrapper can be used in the following way:
rule baserecalibrator:
input:
bam="{sample}.bam",
bai="{sample}.bai",
ref="genome.fasta",
fai="genome.fasta.fai",
dict="genome.dict",
known="dbsnp.vcf.gz",
known_idx="dbsnp.vcf.gz.tbi",
output:
recal_table="{sample}.recal_data_table",
log:
"logs/gatk3/bqsr/{sample}.log",
params:
extra="--defaultBaseQualities 20 --filter_reads_with_N_cigar", # optional
resources:
mem_mb=1024,
threads: 16
wrapper:
"v1.25.0/bio/gatk3/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. “-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.
Software dependencies¶
gatk=3.8
python=3.11.0
snakemake-wrapper-utils=0.5.2
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", "")
log = snakemake.log_fmt_shell(stdout=True, stderr=True)
java_opts = get_java_opts(snakemake)
bed = snakemake.params.get("bed", "")
if bed:
bed = f"--intervals {bed}"
input_known = snakemake.input.get("known", "")
if input_known:
if isinstance(input_known, str):
input_known = [input_known]
input_known = list(map("--knownSites {}".format, input_known))
shell(
"gatk3 {java_opts}"
" --analysis_type BaseRecalibrator"
" --num_cpu_threads_per_data_thread {snakemake.threads}"
" --input_file {snakemake.input.bam}"
" {input_known}"
" --reference_sequence {snakemake.input.ref}"
" {bed}"
" {extra}"
" --out {snakemake.output}"
" {log}"
)