GATK INTERVALLISTTOBED

Run gatk IntervalListToBed.

URL:

Example

This wrapper can be used in the following way:

rule gatk_interval_list_to_bed:
    input:
        intervals="genome.intervals"
    output:
        bed="genome.bed"
    log:
        "logs/genome.log"
    params:
        extra="",
    java_opts="", # optional
    resources:
        mem_mb=1024,
    wrapper:
        "v1.1.0/bio/gatk/intervallisttobed"

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

  • gatk4==4.2.0.0
  • snakemake-wrapper-utils==0.1.3

Input/Output

Input:

  • interval list

Output:

  • bed file

Notes

Authors

  • Filipe G. Vieira

Code

__author__ = "Filipe G. Vieira"
__copyright__ = "Copyright 2021, Filipe G. Vieira"
__license__ = "MIT"


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)
shell(
    "gatk --java-options '{java_opts}' IntervalListToBed --INPUT {snakemake.input.intervals} "
    "{extra} --OUTPUT {snakemake.output.bed} {log}"
)