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:
"v5.8.0-3-g915ba34/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
This program/wrapper does not handle multi-threading.
Software dependencies
bedtools=2.31.1
Input/Output
Input:
BAM file, this must be the first file in the input file list
Output:
BED file, this must be the first file in the output file list
Params
extra
: additional program arguments (except -i)
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}"
)