SAMBAMBA SLICE¶
Fast tool for copying a slice of a BAM file. See details `here https://lomereiter.github.io/sambamba/docs/sambamba-slice.html`_
URL:
Example¶
This wrapper can be used in the following way:
rule sambamba_slice:
input:
bam="mapped/{sample}.bam",
bai="mapped/{sample}.bam.bai"
output:
"mapped/{sample}.region.bam"
params:
region="xx:1-10" # region to catch (contig:start-end)
log:
"logs/sambamba-slice/{sample}.log"
wrapper:
"0.85.0/bio/sambamba/slice"
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¶
sambamba==0.8.0
Input/Output¶
Input:
- coordinate-sorted and indexed bam file
Output:
- new bam file with specific region
Authors¶
- Jan Forster
Code¶
__author__ = "Jan Forster"
__copyright__ = "Copyright 2021, Jan Forster"
__email__ = "j.forster@dkfz.de"
__license__ = "MIT"
import os
from snakemake.shell import shell
log = snakemake.log_fmt_shell(stdout=False, stderr=True)
shell(
"sambamba slice "
"{snakemake.input[0]} {snakemake.params.region} > {snakemake.output[0]} "
"{log}"
)