BEDTOOLS INTERSECT

Intersect BED/BAM/VCF files with bedtools.

URL:

Example

This wrapper can be used in the following way:

rule bedtools_merge:
    input:
        left="A.bed",
        right="B.bed"
    output:
        "A_B.intersected.bed"
    params:
        ## Add optional parameters
        extra="-wa -wb" ## In this example, we want to write original entries in A and B for each overlap.
    log:
        "logs/intersect/A_B.log"
    wrapper:
        "v1.1.0/bio/bedtools/intersect"

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

• bedtools=2.29.0

Authors

• Jan Forster

Code

__author__ = "Jan Forster"
__copyright__ = "Copyright 2019, Jan Forster"
__email__ = "j.forster@dkfz.de"
__license__ = "MIT"

from snakemake.shell import shell

## Extract arguments
extra = snakemake.params.get("extra", "")
log = snakemake.log_fmt_shell(stdout=True, stderr=True)

shell(
    "(bedtools intersect"
    " {extra}"
    " -a {snakemake.input.left}"
    " -b {snakemake.input.right}"
    " > {snakemake.output})"
    " {log}"
)