SLOPBED
Increase the size of each feature in a BED/BAM/VCF by a specified factor.
URL: https://bedtools.readthedocs.io/en/latest/content/tools/slop.html
Example
This wrapper can be used in the following way:
rule bedtools_merge:
input:
"A.bed"
output:
"A.slop.bed"
params:
## Genome file, tab-seperated file defining the length of every contig
genome="genome.txt",
## Add optional parameters
extra = "-b 10" ## in this example, we want to increase the feature by 10 bases to both sides
log:
"logs/slop/A.log"
wrapper:
"v4.6.0-24-g250dd3e/bio/bedtools/slop"
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
Extra parameters requires either -b or (-l and -r)
This program/wrapper does not handle multi-threading.
Software dependencies
bedtools=2.31.1
Input/Output
Input:
Path to an interval file (BED/GFF/VCF)
Output:
Path to the expanded intervals file
Params
genome
: Path to a genome fileextra
: additional program arguments (except for -i or -g)
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 slop"
" {extra}"
" -i {snakemake.input[0]}"
" -g {snakemake.params.genome}"
" > {snakemake.output})"
" {log}"
)