SAMTOOLS STATS¶
Generate stats using samtools. For more information see SAMtools documentation.
Example¶
This wrapper can be used in the following way:
rule samtools_stats:
input:
"mapped/{sample}.bam"
output:
"samtools_stats/{sample}.txt"
params:
extra="", # Optional: extra arguments.
region="xx:1000000-2000000" # Optional: region string.
log:
"logs/samtools_stats/{sample}.log"
wrapper:
"0.71.0/bio/samtools/stats"
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¶
samtools==1.10
Authors¶
- Julian de Ruiter
Code¶
"""Snakemake wrapper for trimming paired-end reads using cutadapt."""
__author__ = "Julian de Ruiter"
__copyright__ = "Copyright 2017, Julian de Ruiter"
__email__ = "julianderuiter@gmail.com"
__license__ = "MIT"
from snakemake.shell import shell
extra = snakemake.params.get("extra", "")
region = snakemake.params.get("region", "")
log = snakemake.log_fmt_shell(stdout=False, stderr=True)
shell("samtools stats {extra} {snakemake.input} {region} > {snakemake.output} {log}")