GATK BASERECALIBRATOR

Run gatk BaseRecalibrator and ApplyBQSR in one step.

Software dependencies

  • gatk4 ==4.1.4.1
  • openjdk =8

Example

This wrapper can be used in the following way:

rule gatk_bqsr:
    input:
        bam="mapped/{sample}.bam",
        ref="genome.fasta",
        known="dbsnp.vcf.gz"  # optional known sites
    output:
        bam="recal/{sample}.bam"
    log:
        "logs/gatk/bqsr/{sample}.log"
    params:
        extra="",  # optional
        java_opts="", # optional
    wrapper:
        "0.50.4/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

Authors

  • Johannes Köster
  • Jake VanCampen

Code

__author__ = "Johannes Köster"
__copyright__ = "Copyright 2018, Johannes Köster"
__email__ = "johannes.koester@protonmail.com"
__license__ = "MIT"


from tempfile import TemporaryDirectory
import os

from snakemake.shell import shell

extra = snakemake.params.get("extra", "")
java_opts = snakemake.params.get("java_opts", "")

with TemporaryDirectory() as tmpdir:
    recal_table = os.path.join(tmpdir, "recal_table.grp")
    log = snakemake.log_fmt_shell(stdout=True, stderr=True)
    known = snakemake.input.get("known", "")
    if known:
        known = "--known-sites {}".format(known)

    shell(
        "gatk --java-options '{java_opts}' BaseRecalibrator {extra} "
        "-R {snakemake.input.ref} -I {snakemake.input.bam} "
        "-O {recal_table} {known} {log}"
    )

    log = snakemake.log_fmt_shell(stdout=True, stderr=True, append=True)
    shell(
        "gatk --java-options '{java_opts}' ApplyBQSR -R {snakemake.input.ref} -I {snakemake.input.bam} "
        "--bqsr-recal-file {recal_table} "
        "-O {snakemake.output.bam} {log}"
    )