BAMTOBED¶
Conversion utility that converts sequence alignments in BAM format into BED, BED12, and/or BEDPE records.
URL: https://bedtools.readthedocs.io/en/latest/content/tools/bamtobed.html
Example¶
This wrapper can be used in the following way:
rule bamtobed:
input:
"{sample}.bam",
output:
"{sample}.bed",
log:
"logs/bamtobed/{sample}.log",
params:
extra="-bedpe", # optional parameters
wrapper:
"v1.19.1/bio/bedtools/bamtobed"
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 extra param allows for additional program arguments.
Software dependencies¶
bedtools=2.30.0
Authors¶
- Filipe G. Vieira
Code¶
__author__ = "Filipe G. Vieira"
__copyright__ = "Copyright 2022, Filipe G. Vieira"
__license__ = "MIT"
from snakemake.shell import shell
log = snakemake.log_fmt_shell(stdout=False, stderr=True)
extra = snakemake.params.get("extra", "")
shell(
"(bamToBed"
" {extra}"
" -i {snakemake.input[0]}"
" > {snakemake.output[0]}"
") {log}"
)